Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/getWigData.xml @ 38:2c0c0a89fad7
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| author | m-zytnicki |
|---|---|
| date | Thu, 02 May 2013 09:56:47 -0400 |
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| 37:d22fadc825e3 | 38:2c0c0a89fad7 |
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| 1 <tool id="getWigData" name="get WIG data"> | |
| 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"> | |
| 7 ../Java/Python/getWigData.py -i $inputGff3File -f gff3 -w $inputWigFile -t $tagName -$strand -o $outputFile | |
| 8 </command> | |
| 9 | |
| 10 <inputs> | |
| 11 <param name="inputGff3File" type="data" label="Input Gff3 File" format="gff3"/> | |
| 12 <param name="inputWigFile" type="data" label="Input Wig File" 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."/> | |
| 14 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately."/> | |
| 15 </inputs> | |
| 16 | |
| 17 <outputs> | |
| 18 <data format="gff3" name="outputFile" label="[get WIG data] output file"/> | |
| 19 </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> |