Mercurial > repos > yufei-luo > s_mart

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents 440ceca58672
children 0ab839023fe4
comparison
equal deleted inserted replaced
17:b0e8584489e6 18:94ab73e8a190
1 <tool id="getWigData" name="get wig data"> 1 <tool id="getWigData" name="get WIG data">
2 <description>Compute the average data for some genomic coordinates using WIG files</description> 2 <description>Compute the average data for some genomic coordinates using WIG files</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
3 <command interpreter="python"> 6 <command interpreter="python">
4 ../Java/Python/getWigData.py -i $inputGff3File -f gff3 -w $inputWigFile -t $tagName -$strand -o $outputFile 7 ../Java/Python/getWigData.py -i $inputGff3File -f gff3 -w $inputWigFile -t $tagName -$strand -o $outputFile
5 </command> 8 </command>
6 9
7 <inputs> 10 <inputs>
10 <param name="tagName" type="text" value="None" label="tag option" help="choose a tag name to write the wig information to output file."/> 13 <param name="tagName" type="text" value="None" label="tag option" help="choose a tag name to write the wig information to output file."/>
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 format="gff3" name="outputFile" label="[getWigData -> gff3] Output File"/> 18 <data format="gff3" name="outputFile" label="[get WIG data] output file"/>
16 </outputs> 19 </outputs>
17 20
18 <help> 21 <help>
19 Reads a transcript list, computes the average value of some WIG data (please consult http://genome.ucsc.edu/goldenPath/help/wiggle.html to know more about this format) for each transcript and adds a tag corresponding to this average value to the transcript. 22 Reads a transcript list, computes the average value of some WIG data (please consult http://genome.ucsc.edu/goldenPath/help/wiggle.html to know more about this format) for each transcript and adds a tag corresponding to this average value to the transcript.
20 23