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comparison SMART/galaxy/getWigData.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="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>
6 <command interpreter="python"> 3 <command interpreter="python">
7 ../Java/Python/getWigData.py -i $inputGff3File -f gff3 -w $inputWigFile -t $tagName -$strand -o $outputFile 4 ../Java/Python/getWigData.py -i $inputGff3File -f gff3 -w $inputWigFile -t $tagName -$strand -o $outputFile
8 </command> 5 </command>
9 6
10 <inputs> 7 <inputs>
11 <param name="inputGff3File" type="data" label="Input Gff3 File" format="gff3"/> 8 <param name="inputGff3File" type="data" label="Input Gff3 File (compulsory option)" format="gff3"/>
12 <param name="inputWigFile" type="data" label="Input Wig File" format="wig"/> 9 <param name="inputWigFile" type="data" label="Input Wig File (compulsory option)" format="wig"/>
13 <param name="tagName" type="text" value="None" label="tag option" help="choose a tag name to write the wig information to output file."/> 10 <param name="tagName" type="text" value="None" label="tag option (compulsory option)" help="choose a tag name to write the wig information to output file."/>
14 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately."/> 11 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately."/>
15 </inputs> 12 </inputs>
16 13
17 <outputs> 14 <outputs>
18 <data format="gff3" name="outputFile" label="[get WIG data] output file"/> 15 <data format="gff3" name="outputFile" label="[getWigData -> gff3] Output File"/>
19 </outputs> 16 </outputs>
20
21 <help>
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.
23
24 The script finds all the data which correspond to the genomic coordinates of a transcript, average these data and store the result into a tag. Then, the transcripts are written in an output file, together with the tag.
25
26 You can then plot your data using *plotTranscriptList.py*.
27 </help>
28 </tool> 17 </tool>