Mercurial > repos > yufei-luo > s_mart
view SMART/galaxy/getWigData.xml @ 58:5f5c9b74c2dd
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author | m-zytnicki |
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date | Fri, 07 Feb 2014 11:53:36 -0500 |
parents | 2c0c0a89fad7 |
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<tool id="getWigData" name="get WIG data"> <description>Compute the average data for some genomic coordinates using WIG files</description> <requirements> <requirement type="set_environment">PYTHONPATH</requirement> </requirements> <command interpreter="python"> ../Java/Python/getWigData.py -i $inputGff3File -f gff3 -w $inputWigFile -t $tagName -$strand -o $outputFile </command> <inputs> <param name="inputGff3File" type="data" label="Input Gff3 File" format="gff3"/> <param name="inputWigFile" type="data" label="Input Wig File" format="wig"/> <param name="tagName" type="text" value="None" label="tag option" help="choose a tag name to write the wig information to output file."/> <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately."/> </inputs> <outputs> <data format="gff3" name="outputFile" label="[get WIG data] output file"/> </outputs> <help> 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. 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. You can then plot your data using *plotTranscriptList.py*. </help> </tool>