Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/changeGffFeatures.xml @ 31:0ab839023fe4

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
comparison
equal deleted inserted replaced
30:5677346472b5 31:0ab839023fe4
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>Changes one feature name by an other name (the feature name can be found on the 3rd column).</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="bash"> 3 <command interpreter="bash">
7 ../Java/Python/changeGffFeatures.sh $inputFile $inputFeature $outputFeature >$outputFile 4 ../Java/Python/changeGffFeatures.sh $inputFile $inputFeature $outputFeature >$outputFile
8 </command> 5 </command>
9 <inputs> 6 <inputs>
10 <param name="inputFile" type="data" label="Input File" format="gff"/> 7 <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"/> 8 <param name="inputFeature" type="text" value="exon" label="A given feature, you must choose a feature name(on the 3rd column)."/>
12 <param name="outputFeature" type="text" value="exon" label="The new feature"/> 9 <param name="outputFeature" type="text" value="exon" label="You must choose an other feature name(on the 3rd column)."/>
13 </inputs> 10 </inputs>
14 11
15 <outputs> 12 <outputs>
16 <data name="outputFile" format="gff" label="[change GFF features] Output File"/> 13 <data name="outputFile" format="gff" label="[changeGffFeatures] Output File"/>
17 </outputs> 14 </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> 15 </tool>
23 16