Mercurial > repos > yufei-luo > s_mart

diff SMART/galaxy/CleanTranscriptFile.xml @ 18:94ab73e8a190

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Uploaded
author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents 440ceca58672
children 0ab839023fe4
line wrap: on
line diff
--- a/SMART/galaxy/CleanTranscriptFile.xml	Mon Apr 22 11:11:10 2013 -0400
+++ b/SMART/galaxy/CleanTranscriptFile.xml	Mon Apr 29 03:20:15 2013 -0400
@@ -1,5 +1,8 @@
-<tool id="CleanTranscriptFile" name="clean Transcript File">
+<tool id="CleanTranscriptFile" name="clean transcript file">
 	<description>Clean a transcript file so that it is useable for S-MART.</description>
+	<requirements>
+		<requirement type="set_environment">PYTHONPATH</requirement>
+	</requirements>
 	<command interpreter="python"> ../Java/Python/CleanTranscriptFile.py -i $formatType.inputFileName 
 		#if $formatType.FormatInputFileName == 'gff':
 		 	-f gff
@@ -51,6 +54,7 @@
 	<outputs>
 		<data name="outputFile" format="gtf">
 			<change_format>
+			<when input="formatType.FormatInputFileName" value="gtf" format="gtf" />
 			<when input="formatType.FormatInputFileName" value="gff" format="gff" />
 			<when input="formatType.FormatInputFileName" value="gff3" format="gff3" />
 		</change_format>