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comparison SMART/galaxy/computeCoverage.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 <tool id="ComputeCoverage" name="compute coverage"> 1 <tool id="ComputeCoverage" name="Compute coverage">
2 <description>Compute the coverage of a set with respect to another set.</description> 2 <description>Compute the coverage of a set with respect to another set.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python"> 3 <command interpreter="python">
7 ../Java/Python/ComputeCoverage.py -i $formatType.inputFileName1 4 ../Java/Python/ComputeCoverage.py -i $formatType.inputFileName1
8 #if $formatType.FormatInputFileName1 == 'bed': 5 #if $formatType.FormatInputFileName1 == 'bed':
9 -f bed 6 -f bed
10 #elif $formatType.FormatInputFileName1 == 'gff': 7 #elif $formatType.FormatInputFileName1 == 'gff':
101 <param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Include introns."/> 98 <param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Include introns."/>
102 99
103 </inputs> 100 </inputs>
104 101
105 <outputs> 102 <outputs>
106 <data name="outputFileGff" format="gff3" label="[compute coverage] output file"/> 103 <data name="outputFileGff" format="gff3" label="[computeCoverage] OUTPUT file"/>
107 </outputs> 104 </outputs>
108 105
109 <help>
110 This tool considers a query and a reference files, and gives the coverage of the query file by the reference. The output file is similar to the query file, where a tag **coverage** has been added.
111 </help>
112 </tool> 106 </tool>
113 107