Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/changeGffFeatures.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="changeGffFeatures" name="change GFF features"> | |
| 2 <description>Change a feature in a GFF file (the feature is the 3rd column).</description> | |
| 3 <requirements> | |
| 4 <requirement type="set_environment">PYTHONPATH</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="bash"> | |
| 7 ../Java/Python/changeGffFeatures.sh $inputFile $inputFeature $outputFeature >$outputFile | |
| 8 </command> | |
| 9 <inputs> | |
| 10 <param name="inputFile" type="data" label="Input File" format="gff"/> | |
| 11 <param name="inputFeature" type="text" value="exon" label="The feature you want to change"/> | |
| 12 <param name="outputFeature" type="text" value="exon" label="The new feature"/> | |
| 13 </inputs> | |
| 14 | |
| 15 <outputs> | |
| 16 <data name="outputFile" format="gff" label="[change GFF features] Output File"/> | |
| 17 </outputs> | |
| 18 | |
| 19 <help> | |
| 20 This script changes the third column of a GFF3 file (please refer to http://www.sequenceontology.org/gff3.shtml to know more about this format). | |
| 21 </help> | |
| 22 </tool> | |
| 23 |