--- a/annotateBedWrapper.xml	Sun Dec 02 15:11:35 2012 -0500
+++ b/annotateBedWrapper.xml	Sun Dec 02 15:37:32 2012 -0500
@@ -1,7 +1,7 @@
-<tool id="annotateBed" name="annotateBed">
+<tool id="annotateBed" name="Annotates">
 
-    <description>Annotate BED files with overlapping BED files</description>
-	
+	<description> the depth & breadth of coverage of features from multiple files</description>
+
 	<requirements>
 		<requirement type="binary">annotateBed</requirement>
 		<requirement type="package">bedtools</requirement>
@@ -24,27 +24,33 @@
 
     <inputs>
 
-        <param name="countflag" type="boolean" label="Use count to annotate" truevalue="-count" falsevalue="" />
-        <param format="bed" name="inputRegion" type="data" label="The region to be annotated" />
+        <param format="bed" name="inputRegion" type="data" label="The regions to be annotated is in this file:" />
+        <param name="countflag" type="select" label="What to report in the output: ">
+			<option value="-counts" selected="true">the count of features in each file that overlap the regions</option>
+			<option value="">fraction of the region covered by each feature</option>
+			<option value="-both">Report the counts followed by the % coverage</option>
+		</param>
 		<repeat name="annotateColumn" title="Column">
-			<param name="colname" type="text" label="Column name" />
-			<param name="colfile" type="data" format="bed" label="BED file to annotate for the column" />
+			<param name="colname" type="text" label="Feature name" />
+			<param name="colfile" type="data" format="bed" label="Feature file to annotate for the column" />
 		</repeat>
 
     </inputs>
     <outputs>
-        <data format="bed" name="output" metadata_source="inputRegion" label="${inputRegion.name} annotated" />
+        <data format="bed" name="output" label="${inputRegion.name} annotated" />
     </outputs>
 
 <help>
 
-.. class:: infomark
+**What it does**
 
-IMPORTANT INFORMATION
+This tool is used to annotate the regions in a bed file with features provided in multiple BED files.
 
-----
+..class:: warningmark
 
-WRITE HELP HERE
+This tool requires that bedtools__ has been installed on your system.
+
+-----
 
 </help>