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comparison genomeCoverageBed.xml @ 32:b0d5e752c0c5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
author iuc
date Tue, 05 Sep 2017 09:51:56 -0400
parents c0fbce5dc84a
children ac2040a5e6ff
comparison
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31:cb98f29aa1dc 32:b0d5e752c0c5
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 $input_type.input_type_select == 'bam' 11 @GENOME_FILE_COVERAGE@
12 -ibam '$input_type.input'
13 #else
14 -i '$input_type.input'
15 -g '$input_type.genome'
16 #end if
17 12
18 $split 13 $split
19 $strand 14 $strand
20 15
21 #if str($report.report_select) == "bg": 16 #if str($report.report_select) == "bg":
47 <option value="bed">BED/VCF/GFF</option> 42 <option value="bed">BED/VCF/GFF</option>
48 <option value="bam">BAM</option> 43 <option value="bam">BAM</option>
49 </param> 44 </param>
50 <when value="bed"> 45 <when value="bed">
51 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" /> 46 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" />
52 <expand macro="genome" /> 47 <expand macro="input_conditional_genome_file" />
53 </when> 48 </when>
54 <when value="bam"> 49 <when value="bam">
55 <param format="bam" name="input" type="data" label="BAM file" /> 50 <param format="bam" name="input" type="data" label="BAM file" />
56 </when> 51 </when>
57 </conditional> 52 </conditional>
63 <when value="bg"> 58 <when value="bg">
64 <param name="zero_regions" type="boolean" checked="False" truevalue="-bga" falsevalue="" 59 <param name="zero_regions" type="boolean" checked="False" truevalue="-bga" falsevalue=""
65 label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported. (-bga)" /> 60 label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported. (-bga)" />
66 <param name="scale" type="float" value="1.0" 61 <param name="scale" type="float" value="1.0"
67 label="Scale the coverage by a constant factor" 62 label="Scale the coverage by a constant factor"
68 help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). (-scale)"/> 63 help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). (-scale)" />
69 </when> 64 </when>
70 <when value="hist"> 65 <when value="hist">
71 <param name="max" type="integer" label="Specify max depth" value="0" 66 <param name="max" type="integer" label="Specify max depth" value="0"
72 help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)"/> 67 help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)" />
73 </when> 68 </when>
74 </conditional> 69 </conditional>
75 <expand macro="split" /> 70 <expand macro="split" />
76 <param name="strand" type="select" label="Calculate coverage based on" help="(-strand)"> 71 <param name="strand" type="select" label="Calculate coverage based on" help="(-strand)">
77 <option value="">both strands combined</option> 72 <option value="">both strands combined</option>
97 </outputs> 92 </outputs>
98 <tests> 93 <tests>
99 <test> 94 <test>
100 <param name="input_type_select" value="bed" /> 95 <param name="input_type_select" value="bed" />
101 <param name="input" value="genomeCoverageBed1.bed" ftype="bed" /> 96 <param name="input" value="genomeCoverageBed1.bed" ftype="bed" />
97 <param name="genome_file_opts_selector" value="hist" />
102 <param name="genome" value="genomeCoverageBed1.len" ftype="tabular" /> 98 <param name="genome" value="genomeCoverageBed1.len" ftype="tabular" />
103 <param name="report_select" value="hist" /> 99 <param name="report_select" value="hist" />
104 <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" /> 100 <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" />
105 </test> 101 </test>
106 </tests> 102 </tests>