Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/getWigData.xml @ 15:440ceca58672
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| author | m-zytnicki |
|---|---|
| date | Mon, 22 Apr 2013 11:08:07 -0400 |
| parents | 769e306b7933 |
| children | 94ab73e8a190 |
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| 14:c79b9ae3f65f | 15:440ceca58672 |
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| 3 <command interpreter="python"> | 3 <command interpreter="python"> |
| 4 ../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 |
| 5 </command> | 5 </command> |
| 6 | 6 |
| 7 <inputs> | 7 <inputs> |
| 8 <param name="inputGff3File" type="data" label="Input Gff3 File (compulsory option)" format="gff3"/> | 8 <param name="inputGff3File" type="data" label="Input Gff3 File" format="gff3"/> |
| 9 <param name="inputWigFile" type="data" label="Input Wig File (compulsory option)" format="wig"/> | 9 <param name="inputWigFile" type="data" label="Input Wig File" format="wig"/> |
| 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."/> | 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."/> | 11 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately."/> |
| 12 </inputs> | 12 </inputs> |
| 13 | 13 |
| 14 <outputs> | 14 <outputs> |
| 15 <data format="gff3" name="outputFile" label="[getWigData -> gff3] Output File"/> | 15 <data format="gff3" name="outputFile" label="[getWigData -> gff3] Output File"/> |
| 16 </outputs> | 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> | |
| 17 </tool> | 25 </tool> |