Mercurial > repos > bgruening > deeptools_correct_gc_bias

comparison correctGCBias.xml @ 17:3f84770b69cd draft

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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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16:f177dde2ae22 17:3f84770b69cd
1 <tool id="deeptools_correct_gc_bias" name="correctGCBias" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_correct_gc_bias" name="correctGCBias" version="@WRAPPER_VERSION@.0">
2 <description>uses the output from computeGCBias to generate GC-corrected BAM files</description> 2 <description>uses the output from computeGCBias to generate GC-corrected BAM/CRAM files</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">correctGCBias</token> 4 <token name="@BINARY@">correctGCBias</token>
5 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 ln -s "$bamInput" "local_bamInput.bam" && 10 ln -s "$bamInput" "local_bamInput.bam" &&
11 ln -s "$bamInput.metadata.bam_index" local_bamInput.bam.bai && 11 #if $bamInput.ext == 'bam':
12 ln -s '${bamInput.metadata.bam_index}' local_bamInput.bam.bai &&
13 #else:
14 ln -s '${bamInput.metadata.cram_index}' local_bamInput.bam.crai &&
15 #end if
12 16
13 @BINARY@ 17 @BINARY@
14 @THREADS@ 18 @THREADS@
15 --bamfile local_bamInput.bam 19 --bamfile local_bamInput.bam
16 --GCbiasFrequenciesFile "$GCbiasFrequenciesFile" 20 --GCbiasFrequenciesFile "$GCbiasFrequenciesFile"
29 --correctedFile corrected.bam 33 --correctedFile corrected.bam
30 ]]> 34 ]]>
31 </command> 35 </command>
32 <inputs> 36 <inputs>
33 <param argument="--GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" help="" /> 37 <param argument="--GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" help="" />
34 <param argument="--bamInput" format="bam" type="data" 38 <param argument="--bamInput" format="bam,cram" type="data"
35 label="BAM file" help="This should be same file that was used for computeGCbias." /> 39 label="BAM/CRAM file" help="This should be same file that was used for computeGCbias." />
36 <expand macro="reference_genome_source" /> 40 <expand macro="reference_genome_source" />
37 <expand macro="effectiveGenomeSize" /> 41 <expand macro="effectiveGenomeSize" />
38 <expand macro="region_limit_operation" /> 42 <expand macro="region_limit_operation" />
39 </inputs> 43 </inputs>
40 <outputs> 44 <outputs>
46 <param name="bamInput" value="paired_chr2L.bam" ftype="bam" /> 50 <param name="bamInput" value="paired_chr2L.bam" ftype="bam" />
47 <param name="ref_source" value="history" /> 51 <param name="ref_source" value="history" />
48 <param name="input1" value="sequence.2bit" /> 52 <param name="input1" value="sequence.2bit" />
49 <param name="effectiveGenomeSize_opt" value="specific" /> 53 <param name="effectiveGenomeSize_opt" value="specific" />
50 <param name="effectiveGenomeSize" value="10050" /> 54 <param name="effectiveGenomeSize" value="10050" />
51 <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" lines_diff="100" /> 55 <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" lines_diff="200" />
52 </test> 56 </test>
53 </tests> 57 </tests>
54 <help> 58 <help>
55 <![CDATA[ 59 <![CDATA[
56 60