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comparison genomeCoverageBed.xml @ 7:8e6b7c3597a8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7
author iuc
date Mon, 18 Jul 2016 14:06:15 -0400
parents 607c0576c6ab
children 7308cc546a36
comparison
equal deleted inserted replaced
6:d25966c8ddeb 7:8e6b7c3597a8
1 <tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.0"> 1 <tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.1">
2 <description>compute the coverage over an entire genome</description> 2 <description>compute the coverage over an entire genome</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 bedtools genomecov 10 bedtools genomecov
11 #if $input.ext == "bam" 11 #if $input_type.input_type_select == 'bam'
12 -ibam '$input' 12 -ibam '$input_type.input'
13 #else 13 #else
14 -i '$input' 14 -i '$input_type.input'
15 -g $genome 15 -g '$input_type.genome'
16 #end if 16 #end if
17 17
18 $split 18 $split
19 $strand 19 $strand
20 20
40 40
41 > '$output' 41 > '$output'
42 ]]> 42 ]]>
43 </command> 43 </command>
44 <inputs> 44 <inputs>
45 <param format="bed,bam" name="input" type="data" label="The BAM or BED file from which coverage should be computed"> 45 <conditional name="input_type">
46 <validator type="unspecified_build" /> 46 <param name="input_type_select" type="select" label="Input type">
47 </param> 47 <option value="bed">BED/VCF/GFF</option>
48 <option value="bam">BAM</option>
49 </param>
50 <when value="bed">
51 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" />
52 <expand macro="genome" />
53 </when>
54 <when value="bam">
55 <param format="bam" name="input" type="data" label="BAM file" />
56 </when>
57 </conditional>
48 <conditional name="report"> 58 <conditional name="report">
49 <param name="report_select" type="select" label="Output type"> 59 <param name="report_select" type="select" label="Output type">
50 <option value="bg" selected="true">BedGraph coverage file</option> 60 <option value="bg" selected="true">BedGraph coverage file</option>
51 <option value="hist">Data suiteable for Histogram</option> 61 <option value="hist">Data suiteable for Histogram</option>
52 </param> 62 </param>
60 <when value="hist"> 70 <when value="hist">
61 <param name="max" type="integer" label="Specify max depth" value="0" 71 <param name="max" type="integer" label="Specify max depth" value="0"
62 help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)"/> 72 help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)"/>
63 </when> 73 </when>
64 </conditional> 74 </conditional>
65 <expand macro="genome" />
66 <expand macro="split" /> 75 <expand macro="split" />
67 <param name="strand" type="select" label="Calculate coverage based on" help="(-strand)"> 76 <param name="strand" type="select" label="Calculate coverage based on" help="(-strand)">
68 <option value="">both strands combined</option> 77 <option value="">both strands combined</option>
69 <option value="-strand +">positive strand only</option> 78 <option value="-strand +">positive strand only</option>
70 <option value="-strand -">negative strand only</option> 79 <option value="-strand -">negative strand only</option>
86 </change_format> 95 </change_format>
87 </data> 96 </data>
88 </outputs> 97 </outputs>
89 <tests> 98 <tests>
90 <test> 99 <test>
100 <param name="input_type_select" value="bed" />
91 <param name="input" value="genomeCoverageBed1.bed" ftype="bed" /> 101 <param name="input" value="genomeCoverageBed1.bed" ftype="bed" />
92 <param name="genome" value="genomeCoverageBed1.len" /> 102 <param name="genome" value="genomeCoverageBed1.len" ftype="tabular" />
93 <param name="report_select" value="hist" /> 103 <param name="report_select" value="hist" />
94 <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" /> 104 <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" />
95 </test> 105 </test>
96 </tests> 106 </tests>
97 <help> 107 <help>