Mercurial > repos > nilesh > rseqc

diff geneBody_coverage.xml @ 59:dbedfc5f5a3c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
author iuc
date Sat, 18 Dec 2021 19:41:19 +0000
parents f437057e46f1
children 1421603cc95b
line wrap: on
line diff
--- a/geneBody_coverage.xml	Thu Nov 28 15:56:37 2019 -0500
+++ b/geneBody_coverage.xml	Sat Dec 18 19:41:19 2021 +0000
@@ -1,19 +1,13 @@
-<tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@WRAPPER_VERSION@.3">
-  <description>
-    Read coverage over gene body.
-  </description>
-
-  <macros>
-    <import>rseqc_macros.xml</import>
-  </macros>
-
+<tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@TOOL_VERSION@.3">
+    <description>Read coverage over gene body</description>
+    <expand macro="bio_tools"/>
+    <macros>
+        <import>rseqc_macros.xml</import>
+    </macros>
     <expand macro="requirements" />
-
-  <expand macro="stdio" />
-
-  <version_command><![CDATA[geneBody_coverage.py --version]]></version_command>
-
-  <command><![CDATA[
+    <expand macro="stdio" />
+    <version_command><![CDATA[geneBody_coverage.py --version]]></version_command>
+    <command><![CDATA[
     #if str($batch_mode.batch_mode_selector) == "merge":
         #import re
         #set $input_list = []
@@ -74,7 +68,7 @@
       <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="outputr" file="output.geneBodyCoverage_r" />
       <output name="outputtxt" file="output.geneBodyCoverage.txt" />
     </test>
     <test>
@@ -82,11 +76,11 @@
         <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" />
+      <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="outputr" file="output2.geneBodyCoverage_r" />
       <output name="outputtxt" file="output2.geneBodyCoverage.txt" />
     </test>