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- Fix indentation - Rename readreduce - Add suite
galaxyproject · Jul 9, 2019 · 9a6adfe · 9a6adfe
1 parent f009487
commit 9a6adfe
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Showing 3 changed files with 34 additions and 26 deletions.
diff --git a/tools/tn93/.shed.yml b/tools/tn93/.shed.yml
@@ -9,3 +9,11 @@ homepage_url: https://github.com/veg/tn93/
 type: unrestricted
 categories:
  - Sequence Analysis
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for the TN-93 tool: {{ tool_name }}"
+suite:
+  name: "suite_tn93"
+  description: "TN-93 – Transmission Analysis by Distance Clustering"
+  long_description: |
+    TN-93 uses the 1993 Tamura-Nei model to deduce pathogen transmission by genetic distance estimation.
diff --git a/tools/tn93/readreduce.xml b/tools/tn93/readreduce.xml
@@ -1,4 +1,4 @@
-<tool id="readreduce" name="Merge matching reads" version="1.0.4">
+<tool id="tn93_readreduce" name="Merge matching reads" version="1.0.4">
     <description>into clusters with TN-93</description>
     <requirements>
         <requirement type="package" version="1.0.4">tn93</requirement>
@@ -7,17 +7,17 @@
     <command detect_errors="exit_code"><![CDATA[
     readreduce
     -q
-        -o '$output'
-        #if str($options.advanced) == 'advanced':
-            -a $options.ambigs
-            -l $options.overlap
-            #if $options.counts_in_name:
-                -d '$options.counts_in_name'
-            #end if
-            -s '$size'
+    -o '$output'
+    #if str($options.advanced) == 'advanced':
+        -a $options.ambigs
+        -l $options.overlap
+        #if $options.counts_in_name:
+            -d '$options.counts_in_name'
         #end if
-        '$input'
-        ]]></command>
+        -s '$size'
+    #end if
+    '$input'
+    ]]></command>
     <inputs>
         <param name="input" type="data" format="fasta" label="Input in FASTA format" />
         <conditional name="options">

diff --git a/tools/tn93/tn93.xml b/tools/tn93/tn93.xml
@@ -6,22 +6,22 @@
     <version_command><![CDATA[tn93 --version]]></version_command>
     <command detect_errors="exit_code"><![CDATA[
     tn93
-        -o '$tn93_distances'
-        #if str($options.advanced) == 'advanced':
-            -t $options.threshold
-            -a $options.ambigs
-            -g $options.fraction
-            -f csv
-            -l $options.overlap
-            #if $options.counts_in_name:
-                -d '$options.counts_in_name'
-            #end if
+    -o '$tn93_distances'
+    #if str($options.advanced) == 'advanced':
+        -t $options.threshold
+        -a $options.ambigs
+        -g $options.fraction
+        -f csv
+        -l $options.overlap
+        #if $options.counts_in_name:
+            -d '$options.counts_in_name'
         #end if
-        #if $second_fasta:
-            -s '$second_fasta'
-        #end if
-        '$input_fasta'
-        ]]></command>
+    #end if
+    #if $second_fasta:
+        -s '$second_fasta'
+    #end if
+    '$input_fasta'
+    ]]></command>
     <inputs>
         <param name="input_fasta" type="data" format="fasta" label="Input in FASTA format" />
         <param name="second_fasta" argument="-s" type="data" format="fasta" optional="true"