Mercurial > repos > bgruening > deeptools_correct_gc_bias
diff correctGCBias.xml @ 17:3f84770b69cd draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
author | bgruening |
---|---|
date | Thu, 15 Feb 2018 07:44:32 -0500 |
parents | 297bccb7d5c6 |
children | 9e60bf557373 |
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--- a/correctGCBias.xml Mon Feb 05 11:43:07 2018 -0500 +++ b/correctGCBias.xml Thu Feb 15 07:44:32 2018 -0500 @@ -1,5 +1,5 @@ <tool id="deeptools_correct_gc_bias" name="correctGCBias" version="@WRAPPER_VERSION@.0"> - <description>uses the output from computeGCBias to generate GC-corrected BAM files</description> + <description>uses the output from computeGCBias to generate GC-corrected BAM/CRAM files</description> <macros> <token name="@BINARY@">correctGCBias</token> <import>deepTools_macros.xml</import> @@ -8,7 +8,11 @@ <command> <![CDATA[ ln -s "$bamInput" "local_bamInput.bam" && - ln -s "$bamInput.metadata.bam_index" local_bamInput.bam.bai && + #if $bamInput.ext == 'bam': + ln -s '${bamInput.metadata.bam_index}' local_bamInput.bam.bai && + #else: + ln -s '${bamInput.metadata.cram_index}' local_bamInput.bam.crai && + #end if @BINARY@ @THREADS@ @@ -31,8 +35,8 @@ </command> <inputs> <param argument="--GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" help="" /> - <param argument="--bamInput" format="bam" type="data" - label="BAM file" help="This should be same file that was used for computeGCbias." /> + <param argument="--bamInput" format="bam,cram" type="data" + label="BAM/CRAM file" help="This should be same file that was used for computeGCbias." /> <expand macro="reference_genome_source" /> <expand macro="effectiveGenomeSize" /> <expand macro="region_limit_operation" /> @@ -48,7 +52,7 @@ <param name="input1" value="sequence.2bit" /> <param name="effectiveGenomeSize_opt" value="specific" /> <param name="effectiveGenomeSize" value="10050" /> - <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" lines_diff="100" /> + <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" lines_diff="200" /> </test> </tests> <help>