Mercurial > repos > bgruening > deeptools_correct_gc_bias

comparison correctGCBias.xml @ 19:9e60bf557373 draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754
author bgruening
date Thu, 05 Apr 2018 10:55:12 -0400
parents 3f84770b69cd
children 5bffaa8354a1
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18:cef5cec10544 19:9e60bf557373
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 #if $bamInput.ext == 'bam': 11 #if $bamInput.ext == 'bam':
12 ln -s '${bamInput.metadata.bam_index}' local_bamInput.bam.bai && 12 ln -s '${bamInput.metadata.bam_index}' local_bamInput.bam.bai &&
13 #else: 13 #else:
14 ln -s '${bamInput.metadata.cram_index}' local_bamInput.bam.crai && 14 ln -s '${bamInput.metadata.cram_index}' local_bamInput.bam.crai &&
15 #end if 15 #end if
16 16
17 @BINARY@ 17 @BINARY@
18 @THREADS@ 18 @THREADS@
19 --bamfile local_bamInput.bam 19 --bamfile local_bamInput.bam
20 --GCbiasFrequenciesFile "$GCbiasFrequenciesFile" 20 --GCbiasFrequenciesFile '$GCbiasFrequenciesFile'
21 21
22 @reference_genome_source@ 22 @reference_genome_source@
23 23
24 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific": 24 #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
25 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize 25 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize