--- a/annotateBedWrapper.xml	Sun Dec 02 14:37:51 2012 -0500
+++ b/annotateBedWrapper.xml	Sun Dec 02 14:38:33 2012 -0500
@@ -2,14 +2,19 @@
 
     <description>TYPE_DESCRIPTION_HERE</description>
 
-    <command interpreter="bash">
-	names=""
-	inputfiles=""
-	#for $i, $s in enumerate($annotateColumn)
-		names=$names + ${s.colname} + " "
-		inputfiles=$inputfiles+ ${s.colfile} + " "
+    <command>
+	bedtools annotate 
+	$countflag
+	-i '$inputRegion'
+	-names 
+	#for $s in enumerate($annotateColumn)
+		${s.colname}
 	#end for
-	bedtools annotate $countflag -names $names -i $inputRegion -files $inputfiles
+	-files
+	#for $s in enumerate($annotateColumn)
+		${s.colfile}
+	#end for
+	&gt; '$output'
 	</command>
 
     <inputs>
@@ -22,11 +27,8 @@
 		</repeat>
 
     </inputs>
-
     <outputs>
-
-        <data format="bed" name="output" />
-  
+        <data format="bed" name="output" metadata_source="input" label="${inputRegion.name} annotated" />
     </outputs>
 
 <help>