--- a/annotateBedWrapper.xml	Sun Dec 02 14:55:10 2012 -0500
+++ b/annotateBedWrapper.xml	Sun Dec 02 15:11:35 2012 -0500
@@ -4,6 +4,7 @@
 	
 	<requirements>
 		<requirement type="binary">annotateBed</requirement>
+		<requirement type="package">bedtools</requirement>
 	</requirements>
 
     <command>
@@ -12,11 +13,11 @@
 	-i '$inputRegion'
 	-names 
 	#for $i, $s in enumerate($annotateColumn)
-		${s.colname}
+		'${s.colname}'
 	#end for
 	-files
 	#for $i, $s in enumerate($annotateColumn)
-		${s.colfile}
+		'${s.colfile}'
 	#end for
 	&gt; '$output'
 	</command>