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comparison windowBed.xml @ 11:7308cc546a36 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
author iuc
date Mon, 17 Oct 2016 10:13:35 -0400
parents 607c0576c6ab
children fadebae7e69b
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10:c78cf6fe3018 11:7308cc546a36
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 bedtools window 10 bedtools window
11 #if $inputA.ext == "bam": 11 #if $inputA.ext == "bam":
12 -abam $inputA 12 -abam '$inputA'
13 #else: 13 #else:
14 -a $inputA 14 -a '$inputA'
15 #end if 15 #end if
16 -b $inputB 16 -b '$inputB'
17 $bed 17 $bed
18 $strandB 18 $strandB
19 #if $addition.addition_select == 'window': 19 #if $addition.addition_select == 'window':
20 -w $addition.w 20 -w $addition.w
21 #elif $addition.addition_select == 'lr': 21 #elif $addition.addition_select == 'lr':
24 #end if 24 #end if
25 $original 25 $original
26 $number 26 $number
27 $nooverlaps 27 $nooverlaps
28 $header 28 $header
29 > $output 29 > '$output'
30 ]]> 30 ]]>
31 </command> 31 </command>
32 <inputs> 32 <inputs>
33 <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF/BAM file"/> 33 <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF/BAM file"/>
34 <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/> 34 <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>