Mercurial > repos > nilesh > rseqc
diff geneBody_coverage.xml @ 59:dbedfc5f5a3c draft
"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 |
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--- 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>