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comparison coverageBed.xml @ 36:1133660b0f9d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a
author iuc
date Wed, 10 Jan 2018 19:21:14 -0500
parents ac2040a5e6ff
children 58451dcd076d
comparison
equal deleted inserted replaced
35:ac2040a5e6ff 36:1133660b0f9d
1 <tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.0"> 1 <tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1">
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" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 #set inputBs = "' '".join([str($file) for $file in $inputB])
11
12 bedtools coverage 10 bedtools coverage
13 $d 11 $d
14 $hist 12 $hist
15 $split 13 $split
16 $strandedness 14 $strandedness
21 -F '$overlap_b' 19 -F '$overlap_b'
22 #end if 20 #end if
23 $reciprocal_overlap 21 $reciprocal_overlap
24 $a_or_b 22 $a_or_b
25 -a '$inputA' 23 -a '$inputA'
26 -b '$inputBs' 24 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
25 -b '$reduce_or_iterate.inputB'
26 #else:
27 #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB])
28 -b '$inputBs'
29 #end if
27 | sort -k1,1 -k2,2n 30 | sort -k1,1 -k2,2n
28 > '$output' 31 > '$output'
29 ]]> 32 ]]>
30 </command> 33 </command>
31 <inputs> 34 <inputs>
32 <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" /> 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" />
33 <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true" label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format" /> 36 <conditional name="reduce_or_iterate">
37 <param name='reduce_or_iterate_selector' type='select' label='Combined or separate output files'>
38 <option value='iterate' selected='true'>One output file per 'input B' file</option>
39 <option value='reduce'>Single output containing results for all 'input B' files</option>
40 </param>
41 <when value='iterate'>
42 <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data"
43 label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format"/>
44 </when>
45 <when value='reduce'>
46 <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true"
47 label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format"/>
48 </when>
49 </conditional>
34 <expand macro="split" /> 50 <expand macro="split" />
35 <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false" 51 <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false"
36 help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand (-s)"/> 52 help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand (-s)"/>
37 <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue="" 53 <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue=""
38 label="Report the depth at each position in each A feature" 54 label="Report the depth at each position in each A feature"