annotate SMART/galaxy/changeGffFeatures.xml @ 58:5f5c9b74c2dd

Uploaded
author m-zytnicki
date Fri, 07 Feb 2014 11:53:36 -0500
parents 2c0c0a89fad7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
38
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
1 <tool id="changeGffFeatures" name="change GFF features">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
2 <description>Change a feature in a GFF file (the feature is the 3rd column).</description>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
3 <requirements>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
4 <requirement type="set_environment">PYTHONPATH</requirement>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
5 </requirements>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
6 <command interpreter="bash">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
7 ../Java/Python/changeGffFeatures.sh $inputFile $inputFeature $outputFeature >$outputFile
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
8 </command>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
9 <inputs>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
10 <param name="inputFile" type="data" label="Input File" format="gff"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
11 <param name="inputFeature" type="text" value="exon" label="The feature you want to change"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
12 <param name="outputFeature" type="text" value="exon" label="The new feature"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
13 </inputs>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
14
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
15 <outputs>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
16 <data name="outputFile" format="gff" label="[change GFF features] Output File"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
17 </outputs>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
18
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
19 <help>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
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).
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
21 </help>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
22 </tool>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
23