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comparison SMART/galaxy/computeCoverage.xml @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents 440ceca58672
children 0ab839023fe4
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17:b0e8584489e6 18:94ab73e8a190
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>
3 <command interpreter="python"> 6 <command interpreter="python">
4 ../Java/Python/ComputeCoverage.py -i $formatType.inputFileName1 7 ../Java/Python/ComputeCoverage.py -i $formatType.inputFileName1
5 #if $formatType.FormatInputFileName1 == 'bed': 8 #if $formatType.FormatInputFileName1 == 'bed':
6 -f bed 9 -f bed
7 #elif $formatType.FormatInputFileName1 == 'gff': 10 #elif $formatType.FormatInputFileName1 == 'gff':
98 <param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Include introns."/> 101 <param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Include introns."/>
99 102
100 </inputs> 103 </inputs>
101 104
102 <outputs> 105 <outputs>
103 <data name="outputFileGff" format="gff3" label="[computeCoverage] OUTPUT file"/> 106 <data name="outputFileGff" format="gff3" label="[compute coverage] output file"/>
104 </outputs> 107 </outputs>
105 108
106 <help> 109 <help>
107 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. 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.
108 </help> 111 </help>