--- a/SMART/galaxy/modifyGenomicCoordinates.xml	Mon Apr 29 03:45:52 2013 -0400
+++ b/SMART/galaxy/modifyGenomicCoordinates.xml	Tue Apr 30 14:33:21 2013 -0400
@@ -1,8 +1,5 @@
 <tool id="modifyGenomicCoordinates" name="modify genomic coordinates">
   <description>Extend or shrink a list of genomic coordinates.</description>
-	<requirements>
-		<requirement type="set_environment">PYTHONPATH</requirement>
-	</requirements>
   <command interpreter="python"> ../Java/Python/modifyGenomicCoordinates.py -i $formatType.inputFileName
 		#if $formatType.FormatInputFileName == 'bed':
 			-f bed
@@ -69,7 +66,7 @@
 		</conditional>
   
 		<conditional name="OptionStart">
-			<param name="start" type="select" label="shrink to the start of the feature">
+			<param name="start" type="select" label="restrict to the start of the transcript">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
@@ -81,7 +78,7 @@
 		</conditional>
 		
 		<conditional name="OptionEnd">
-			<param name="end" type="select" label="shrink to the end of the feature">
+			<param name="end" type="select" label="restrict to the end of the transcript">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
@@ -121,18 +118,9 @@
   </inputs>
 
   <outputs>
-    <data format="gff3" name="outputFile" label="[modify genomic coordinates] output file"/>
+    <data format="gff3" name="outputFile" label="[modifyGenomicCoordinates] Output File"/>
   </outputs>
 
   <help>
-This tool reads a list of transcripts and modifies each feature by:
-
-- shrinking it to the *n* first nucleotides or the *n* last nucleotides, or
-
-- extending it to *n* nucleotides towards the 5' direction (upstream) or the 3' direction (downstream).
-
-Note that the 5' or 3' direction depends on the orientation of the feature (the 5' end of a transcript located on the minus strand is on the right hand of this transcript!).
-
-The tool needs a transcript file, its format, and outputs a new transcript file.
   </help>
 </tool>