Mercurial > repos > yufei-luo > s_mart

diff SMART/galaxy/changeGffFeatures.xml @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/changeGffFeatures.xml	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,23 @@
+<tool id="changeGffFeatures" name="change GFF features">
+	<description>Change a feature in a GFF file (the feature is the 3rd column).</description>
+		<requirements>
+			<requirement type="set_environment">PYTHONPATH</requirement>
+		</requirements>
+		<command interpreter="bash">
+			../Java/Python/changeGffFeatures.sh $inputFile $inputFeature $outputFeature >$outputFile
+		</command>
+      <inputs>
+	      <param name="inputFile" type="data" label="Input File" format="gff"/>	
+	      <param name="inputFeature" type="text" value="exon" label="The feature you want to change"/>
+	      <param name="outputFeature" type="text" value="exon" label="The new feature"/>
+      </inputs>
+
+      <outputs>
+             <data name="outputFile" format="gff" label="[change GFF features] Output File"/>
+      </outputs> 
+
+	  <help>
+		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).
+	  </help>
+</tool>
+