diff geneBody_coverage.xml @ 12:57fad5deeb8e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"

--- a/geneBody_coverage.xml	Wed Sep 01 08:21:45 2021 +0000
+++ b/geneBody_coverage.xml	Sat Dec 18 19:40:16 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@WRAPPER_VERSION@.3">
+<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>
@@ -68,7 +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>
@@ -76,11 +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>