Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/getWigDistance.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="getWigDistance" name="get wig distance"> 1 <tool id="getWigDistance" name="get WIG distance">
2 <description>Compute the average data around some genomic coordinates using WIG files (thus covering a large proportion of the genome).</description> 2 <description>Compute the average data around some genomic coordinates using WIG files (thus covering a large proportion of the genome).</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
3 <command interpreter="python"> 6 <command interpreter="python">
4 ../Java/Python/getWigDistance.py -i $inputGff3File -f gff3 -w $inputWigFile -a 0.0 -d $distance $strand -o $outputFile 7 ../Java/Python/getWigDistance.py -i $inputGff3File -f gff3 -w $inputWigFile -a 0.0 -d $distance $strand -o $outputFile
5 </command> 8 </command>
6 9
7 <inputs> 10 <inputs>
10 <param name="distance" type="integer" value="1000" label="Distance around positions."/> 13 <param name="distance" type="integer" value="1000" label="Distance around positions."/>
11 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Consider both strands separately."/> 14 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Consider both strands separately."/>
12 </inputs> 15 </inputs>
13 16
14 <outputs> 17 <outputs>
15 <data name="outputFile" format="png" label="[getWigDistance] PNG output File"/> 18 <data name="outputFile" format="png" label="[get WIG distance] PNG output file"/>
16 </outputs> 19 </outputs>
17 20
18 <help> 21 <help>
19 Plots the average data contained in a set of WIG files (please consult http://genome.ucsc.edu/goldenPath/help/wiggle.html to know more about this format) around the first nucleotides of a annotation file. 22 Plots the average data contained in a set of WIG files (please consult http://genome.ucsc.edu/goldenPath/help/wiggle.html to know more about this format) around the first nucleotides of a annotation file.
20 23