--- a/SMART/galaxy/CleanTranscriptFile.xml	Mon Apr 29 03:45:52 2013 -0400
+++ b/SMART/galaxy/CleanTranscriptFile.xml	Tue Apr 30 14:33:21 2013 -0400
@@ -1,8 +1,5 @@
-<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>
+<tool id="CleanTranscriptFile" name="Clean Transcript File">
+	<description> Clean a transcript file so that it is useable for S-MART.</description>
 	<command interpreter="python"> ../Java/Python/CleanTranscriptFile.py -i $formatType.inputFileName 
 		#if $formatType.FormatInputFileName == 'gff':
 		 	-f gff
@@ -54,7 +51,6 @@
 	<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> 
@@ -70,8 +66,4 @@
     </test>
   </tests>
 
-	<help>
-		A GFF/GTF file (please consult http://www.sequenceontology.org/gff3.shtml to know more about the GFF3 format, and http://mblab.wustl.edu/GTF22.html for the GTF format) may contain different sources of information: chromosome size, genes, transcripts, etc. S-MART mostly works on transcripts. This scripts filters the input file to keep the information you really want, based on the feature (3rd column).
-	</help>
-
 </tool>