--- a/SMART/galaxy/mergeTranscriptLists.xml	Mon Apr 29 03:45:52 2013 -0400
+++ b/SMART/galaxy/mergeTranscriptLists.xml	Tue Apr 30 14:33:21 2013 -0400
@@ -1,8 +1,5 @@
 <tool id="mergeTranscriptLists" name="merge transcript lists">
 	<description>Merge the elements of two lists of genomic coordinates.</description>
-	<requirements>
-		<requirement type="set_environment">PYTHONPATH</requirement>
-	</requirements>
 	<command interpreter="python">
 		../Java/Python/mergeTranscriptLists.py -i $formatType.inputFileName1
 		#if $formatType.FormatInputFileName1 == 'bed':
@@ -48,6 +45,9 @@
 		#end if	
 		
 		-o $outputFileGff 
+		
+	
+
 	</command>
 
 	<inputs>
@@ -142,12 +142,7 @@
 	</inputs>
 
 	<outputs>
-		<data name="outputFileGff" format="gff3" label="[merge transcript lists] output file"/>
+		<data name="outputFileGff" format="gff3" label="[mergeTranscriptLists]out file"/>
 	</outputs> 
 	
-	<help>
-The script is similar to *compare overlapping*, except that when data of two different sets overlap, they are merged. You can use the same parameters as *compare overlapping* and use them to look for transcription on both strands, for example.
-
-Optionally, you can also add to the output all the elements from the first set which do not overlap with the second set.
-	</help>
 </tool>