Mercurial > repos > nilesh > rseqc

diff geneBody_coverage.xml @ 63:27e16a30667a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 5968573462fa
children
line wrap: on
line diff
--- a/geneBody_coverage.xml	Wed Feb 22 15:06:01 2023 +0000
+++ b/geneBody_coverage.xml	Tue Apr 09 11:24:55 2024 +0000
@@ -4,8 +4,8 @@
         <import>rseqc_macros.xml</import>
     </macros>
     <expand macro="bio_tools"/>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <version_command><![CDATA[geneBody_coverage.py --version]]></version_command>
     <command><![CDATA[
     #if str($batch_mode.batch_mode_selector) == "merge":
@@ -30,63 +30,58 @@
     #end if
     ]]>
   </command>
-
-  <inputs>
-    <conditional name="batch_mode">
-        <param name="batch_mode_selector" type="select" label="Run each sample separately, or combine mutiple samples into one plot">
-            <option value="batch" selected="true">Run each sample separately</option>
-            <option value="merge">Combine multiple samples into a single plot</option>
-        </param>
-        <when value="batch">
-            <param name="input" type="data" label="Input .bam file" format="bam" help="(--input-file)"/>
-        </when>
-        <when value="merge">
-            <param name="inputs" type="data" label="Input .bam file(s)" format="bam" help="(--input-file)" multiple="true"/>
-        </when>
-    </conditional>
-    <expand macro="refgene_param" />
-    <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length (default: 100)" help="Minimum mRNA length in bp, mRNA that are shorter than this value will be skipped (--minimum_length)." />
-    <expand macro="rscript_output_param" />
-  </inputs>
-
-  <outputs>
-    <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string}: curves (PDF)" />
-    <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string}: heatmap (PDF)">
-      <filter>batch_mode['batch_mode_selector'] == 'merge' and len(inputs) >= 3</filter>
-    </data>
-    <expand macro="rscript_output_data" filename="output.geneBodyCoverage.r" label="${tool.name} on ${on_string}: Rscript"/>
-    <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string}: stats (TXT)" />
-  </outputs>
-
-  <!-- PDF Files contain R version, must avoid checking for diff -->
-  <tests>
-    <test>
-      <conditional name="batch_mode">
-        <param name="batch_mode_selector" value="batch" />
-        <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
-      </conditional>
-      <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" />
-      <param name="rscript_output" value="true" />
-      <output name="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf" compare="sim_size" />
-      <output name="outputr" file="output.geneBodyCoverage_r" />
-      <output name="outputtxt" file="output.geneBodyCoverage.txt" />
-    </test>
-    <test>
-      <conditional name="batch_mode">
-        <param name="batch_mode_selector" value="merge" />
-        <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
-      </conditional>
-      <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
-      <param name="rscript_output" value="true" />
-      <output name="outputcurvespdf" file="output2.geneBodyCoverage.curves.pdf" compare="sim_size" />
-      <output name="outputheatmappdf" file="output2.geneBodyCoverage.heatMap.pdf" compare="sim_size" />
-      <output name="outputr" file="output2.geneBodyCoverage_r" />
-      <output name="outputtxt" file="output2.geneBodyCoverage.txt" />
-    </test>
-
-  </tests>
-
-  <help><![CDATA[
+    <inputs>
+        <conditional name="batch_mode">
+            <param name="batch_mode_selector" type="select" label="Run each sample separately, or combine mutiple samples into one plot">
+                <option value="batch" selected="true">Run each sample separately</option>
+                <option value="merge">Combine multiple samples into a single plot</option>
+            </param>
+            <when value="batch">
+                <param name="input" type="data" label="Input .bam file" format="bam" help="(--input-file)"/>
+            </when>
+            <when value="merge">
+                <param name="inputs" type="data" label="Input .bam file(s)" format="bam" help="(--input-file)" multiple="true"/>
+            </when>
+        </conditional>
+        <expand macro="refgene_param"/>
+        <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length (default: 100)" help="Minimum mRNA length in bp, mRNA that are shorter than this value will be skipped (--minimum_length)."/>
+        <expand macro="rscript_output_param"/>
+    </inputs>
+    <outputs>
+        <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string}: curves (PDF)"/>
+        <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string}: heatmap (PDF)">
+            <filter>batch_mode['batch_mode_selector'] == 'merge' and len(inputs) &gt;= 3</filter>
+        </data>
+        <expand macro="rscript_output_data" filename="output.geneBodyCoverage.r" label="${tool.name} on ${on_string}: Rscript"/>
+        <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string}: stats (TXT)"/>
+    </outputs>
+    <!-- PDF Files contain R version, must avoid checking for diff -->
+    <tests>
+        <test expect_num_outputs="3">
+            <conditional name="batch_mode">
+                <param name="batch_mode_selector" value="batch"/>
+                <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
+            </conditional>
+            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
+            <param name="rscript_output" value="true"/>
+            <output name="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf" compare="sim_size"/>
+            <output name="outputr" file="output.geneBodyCoverage_r"/>
+            <output name="outputtxt" file="output.geneBodyCoverage.txt"/>
+        </test>
+        <test expect_num_outputs="4">
+            <conditional name="batch_mode">
+                <param name="batch_mode_selector" value="merge"/>
+                <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
+            </conditional>
+            <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
+            <param name="rscript_output" value="true"/>
+            <output name="outputcurvespdf" file="output2.geneBodyCoverage.curves.pdf" compare="sim_size"/>
+            <output name="outputheatmappdf" file="output2.geneBodyCoverage.heatMap.pdf" compare="sim_size"/>
+            <output name="outputr" file="output2.geneBodyCoverage_r"/>
+            <output name="outputtxt" file="output2.geneBodyCoverage.txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
 ## geneBody_coverage.py
 
 Read coverage over gene body. This module is used to check if read coverage is uniform and if there is any 5\'/3\' bias. This module scales all transcripts to 100 nt and calculates the number of reads covering each nucleotide position. Finally, it generates plots illustrating the coverage profile along the gene body.
@@ -138,7 +133,5 @@
 
     ]]>
   </help>
-
-  <expand macro="citations" />
-
+    <expand macro="citations"/>
 </tool>