comparison SMART/galaxy/getWigData.xml @ 36:44d5973c188c

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author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
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35:d94018ca4ada 36:44d5973c188c
1 <tool id="getWigData" name="get wig data">
2 <description>Compute the average data for some genomic coordinates using WIG files</description>
3 <command interpreter="python">
4 ../Java/Python/getWigData.py -i $inputGff3File -f gff3 -w $inputWigFile -t $tagName -$strand -o $outputFile
5 </command>
6
7 <inputs>
8 <param name="inputGff3File" type="data" label="Input Gff3 File" format="gff3"/>
9 <param name="inputWigFile" type="data" label="Input Wig File" format="wig"/>
10 <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."/>
12 </inputs>
13
14 <outputs>
15 <data format="gff3" name="outputFile" label="[getWigData -> gff3] Output File"/>
16 </outputs>
17
18 <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.
20
21 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.
22
23 You can then plot your data using *plotTranscriptList.py*.
24 </help>
25 </tool>