--- a/SMART/galaxy/CollapseReads.xml	Fri Apr 19 10:13:11 2013 -0400
+++ b/SMART/galaxy/CollapseReads.xml	Mon Apr 22 11:08:07 2013 -0400
@@ -1,5 +1,5 @@
 <tool id="collapseReads" name="collapse reads">
-	<description>Merges two reads if they have exactly the same genomic coordinates.</description>
+	<description>Merges two genomic features if they have exactly the same genomic coordinates.</description>
 	<command interpreter="python">
 		../Java/Python/CollapseReads.py -i $formatType.inputFileName
 		#if $formatType.FormatInputFileName == 'bed':
@@ -49,11 +49,16 @@
 			</when>
 		</conditional>
 
-		<param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Strand option merges 2 different strands[default:False]."/>
+		<param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Merges features even if they are on different strands."/>
 	</inputs>
 
 	<outputs>
 		<data name="outputFileGff" format="gff3"/>
 	</outputs> 
 	
+	<help>
+Merge two input genomic coordinates iff they are exactly the same. If two or more genomic coordinates are merged, the tag **nbElements** is updated accordingly. As a consequence, all the reads which are exactly the same appear as one genomic coordinate.
+
+This is especially useful for short RNA sequencing (where you want to count the number of read per miRNA, siRNA, etc.) or 5' capped short reads.
+	</help>
 </tool>