dada2: remove datatypes.xml reduce test data size

galaxyproject · Nov 6, 2019 · 9c1efa7 · 9c1efa7
1 parent 67682bd
commit 9c1efa7
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Showing 32 changed files with 52 additions and 476 deletions.
diff --git a/tools/dada2/dada2_plotQualityProfile.xml b/tools/dada2/dada2_plotQualityProfile.xml
@@ -112,8 +112,8 @@ ggsave('output_rev.pdf', qp, width = 20,height = 15,units = c("cm"))
                 </collection>
             </param>
             <param name="batch_cond|aggregate" value="FALSE"/>
-            <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="5000"/>
-            <output name="output_rev" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="5000"/>
+            <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
+            <output name="output_rev" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
         </test>
         <!-- paired-separate joint, no-aggregate (sim_size because element ids differ) -->
         <test expect_num_outputs="2">
@@ -122,8 +122,8 @@ ggsave('output_rev.pdf', qp, width = 20,height = 15,units = c("cm"))
             <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
             <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
             <param name="batch_cond|aggregate" value="FALSE"/>
-            <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="5000"/>
-            <output name="output_rev" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="5000"/>
+            <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
+            <output name="output_rev" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
         </test>
         <!-- single, non-batch, aggregate, small sample -->
         <test expect_num_outputs="1">
@@ -132,7 +132,7 @@ ggsave('output_rev.pdf', qp, width = 20,height = 15,units = c("cm"))
             <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
             <param name="n" value="10000"/>
             <param name="batch_cond|aggregate" value="TRUE"/>
-            <output name="output" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="5000"/>
+            <output name="output" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
         </test>
 
         <!-- paired, batch -->
@@ -145,25 +145,25 @@ ggsave('output_rev.pdf', qp, width = 20,height = 15,units = c("cm"))
                     <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
                 </collection>
             </param>
-            <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="5000"/>
-            <output name="output_rev" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="5000"/>
+            <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
+            <output name="output_rev" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
         </test>
         <!-- paired-separate batch  (sim_size because element ids differ)-->
         <test expect_num_outputs="2">
             <param name="batch_cond|batch_select" value="batch"/>
             <param name="batch_cond|paired_cond|paired_select" value="separate"/>
             <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
             <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
-            <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="5000"/>
-            <output name="output_rev" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="5000"/>
+            <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
+            <output name="output_rev" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
         </test>
         <!-- single, batch -->
         <test expect_num_outputs="1">
             <param name="batch_cond|batch_select" value="batch"/>
             <param name="batch_cond|paired_cond|paired_select" value="single"/>
             <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
             <param name="n" value="10000"/>
-            <output name="output" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="5000"/>
+            <output name="output" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/dada2/datatypes_conf.xml b/tools/dada2/datatypes_conf.xml
diff --git a/tools/dada2/test-data/F3D0_S188_L001_R1_001.fastq.gz b/tools/dada2/test-data/F3D0_S188_L001_R1_001.fastq.gz
diff --git a/tools/dada2/test-data/F3D0_S188_L001_R2_001.fastq.gz b/tools/dada2/test-data/F3D0_S188_L001_R2_001.fastq.gz