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comparison coverageBed.xml @ 40:58451dcd076d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 09721a12bdd393441b162056316241aba3895a4f
author iuc
date Sun, 18 Feb 2018 15:06:49 -0500
parents 1133660b0f9d
children d279800f4ff9
comparison
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39:da6d7bc0a8b0 40:58451dcd076d
1 <tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1"> 1 <tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.2">
2 <description>of features in file B on the features in file A (bedtools coverage)</description> 2 <description>of features in file B on the features in file A (bedtools coverage)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
21 $reciprocal_overlap 21 $reciprocal_overlap
22 $a_or_b 22 $a_or_b
23 -a '$inputA' 23 -a '$inputA'
24 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate': 24 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
25 -b '$reduce_or_iterate.inputB' 25 -b '$reduce_or_iterate.inputB'
26 #if $reduce_or_iterate.inputB.is_of_type('bam'):
27 -sorted -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5)
28 #end if
26 #else: 29 #else:
27 #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB]) 30 #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB])
28 -b '$inputBs' 31 -b '$inputBs'
29 #end if 32 #end if
30 | sort -k1,1 -k2,2n 33 #if $inputA.is_of_type('gff') or $inputA.is_of_type('gff3'):
34 | sort -k1,1 -k4,2n
35 #else:
36 | sort -k1,1 -k2,2n
37 #end if
31 > '$output' 38 > '$output'
32 ]]> 39 ]]>
33 </command> 40 </command>
34 <inputs> 41 <inputs>
35 <param format="bam,bed,gff,gff3,vcf" name="inputA" type="data" label="File A (on which coverage is calculated)" help="BAM/BED/GFF/VCF format" /> 42 <param format="bam,bed,gff,gff3,vcf" name="inputA" type="data" label="File A (on which coverage is calculated)" help="BAM/BED/GFF/VCF format" />