--- a/SMART/galaxy/modifyGenomicCoordinates.xml	Fri Apr 19 10:13:11 2013 -0400
+++ b/SMART/galaxy/modifyGenomicCoordinates.xml	Mon Apr 22 11:08:07 2013 -0400
@@ -66,7 +66,7 @@
 		</conditional>
   
 		<conditional name="OptionStart">
-			<param name="start" type="select" label="restrict to the start of the transcript">
+			<param name="start" type="select" label="shrink to the start of the feature">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
@@ -78,7 +78,7 @@
 		</conditional>
 		
 		<conditional name="OptionEnd">
-			<param name="end" type="select" label="restrict to the end of the transcript">
+			<param name="end" type="select" label="shrink to the end of the feature">
 				<option value="Yes">Yes</option>
 				<option value="No" selected="true">No</option>
 			</param>
@@ -122,5 +122,14 @@
   </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>