Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/changeGffFeatures.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 |
|---|---|
| 1 <tool id="changeGffFeatures" name="change gff Features"> | 1 <tool id="changeGffFeatures" name="change gff Features"> |
| 2 <description>Changes one feature name by an other name (the feature name can be found on the 3rd column).</description> | 2 <description>Change a feature in a GFF file (the feature is the 3rd column).</description> |
| 3 <command interpreter="bash"> | 3 <command interpreter="bash"> |
| 4 ../Java/Python/changeGffFeatures.sh $inputFile $inputFeature $outputFeature >$outputFile | 4 ../Java/Python/changeGffFeatures.sh $inputFile $inputFeature $outputFeature >$outputFile |
| 5 </command> | 5 </command> |
| 6 <inputs> | 6 <inputs> |
| 7 <param name="inputFile" type="data" label="Input File" format="gff"/> | 7 <param name="inputFile" type="data" label="Input File" format="gff"/> |
| 8 <param name="inputFeature" type="text" value="exon" label="A given feature, you must choose a feature name(on the 3rd column)."/> | 8 <param name="inputFeature" type="text" value="exon" label="The feature you want to change"/> |
| 9 <param name="outputFeature" type="text" value="exon" label="You must choose an other feature name(on the 3rd column)."/> | 9 <param name="outputFeature" type="text" value="exon" label="The new feature"/> |
| 10 </inputs> | 10 </inputs> |
| 11 | 11 |
| 12 <outputs> | 12 <outputs> |
| 13 <data name="outputFile" format="gff" label="[changeGffFeatures] Output File"/> | 13 <data name="outputFile" format="gff" label="[changeGffFeatures] Output File"/> |
| 14 </outputs> | 14 </outputs> |
| 15 | |
| 16 <help> | |
| 17 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). | |
| 18 </help> | |
| 15 </tool> | 19 </tool> |
| 16 | 20 |