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comparison SMART/galaxy/changeGffFeatures.xml @ 18:94ab73e8a190

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Uploaded
author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents 440ceca58672
children 0ab839023fe4
comparison
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17:b0e8584489e6 18:94ab73e8a190
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>