--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annotateBedWrapper.xml	Sun Dec 02 15:45:34 2012 -0500
@@ -0,0 +1,58 @@
+<tool id="annotateBed" name="Annotates">
+
+	<description> the depth &amp; breadth of coverage of features from multiple files
+	</description>
+
+	<requirements>
+		<requirement type="binary">annotateBed</requirement>
+		<requirement type="package">bedtools</requirement>
+	</requirements>
+
+    <command>
+	annotateBed 
+	$countflag
+	-i '$inputRegion'
+	-names 
+	#for $i, $s in enumerate($annotateColumn)
+		'${s.colname}'
+	#end for
+	-files
+	#for $i, $s in enumerate($annotateColumn)
+		'${s.colfile}'
+	#end for
+	&gt; '$output'
+	</command>
+
+    <inputs>
+
+        <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="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" label="${inputRegion.name} annotated" />
+    </outputs>
+
+<help>
+
+**What it does**
+
+This tool is used to annotate the regions in a bed file with features provided in multiple BED files.
+
+..class:: warningmark
+
+This tool requires that bedtools__ has been installed on your system.
+
+-----
+
+</help>
+
+</tool>
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