Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/changeGffFeatures.xml @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
parents | 440ceca58672 |
children | 0ab839023fe4 |
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17:b0e8584489e6 | 18:94ab73e8a190 |
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1 <tool id="changeGffFeatures" name="change gff Features"> | 1 <tool id="changeGffFeatures" name="change GFF features"> |
2 <description>Change a feature in a GFF file (the feature is the 3rd column).</description> | 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> | |
3 <command interpreter="bash"> | 6 <command interpreter="bash"> |
4 ../Java/Python/changeGffFeatures.sh $inputFile $inputFeature $outputFeature >$outputFile | 7 ../Java/Python/changeGffFeatures.sh $inputFile $inputFeature $outputFeature >$outputFile |
5 </command> | 8 </command> |
6 <inputs> | 9 <inputs> |
7 <param name="inputFile" type="data" label="Input File" format="gff"/> | 10 <param name="inputFile" type="data" label="Input File" format="gff"/> |
8 <param name="inputFeature" type="text" value="exon" label="The feature you want to change"/> | 11 <param name="inputFeature" type="text" value="exon" label="The feature you want to change"/> |
9 <param name="outputFeature" type="text" value="exon" label="The new feature"/> | 12 <param name="outputFeature" type="text" value="exon" label="The new feature"/> |
10 </inputs> | 13 </inputs> |
11 | 14 |
12 <outputs> | 15 <outputs> |
13 <data name="outputFile" format="gff" label="[changeGffFeatures] Output File"/> | 16 <data name="outputFile" format="gff" label="[change GFF features] Output File"/> |
14 </outputs> | 17 </outputs> |
15 | 18 |
16 <help> | 19 <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). | 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). |
18 </help> | 21 </help> |