# HG changeset patch
# User xiaoyi-cao
# Date 1354468305 18000
# Node ID 0cba7d8f48abf8516aceba9d1253925a5ff76054

Uploaded

diff -r 000000000000 -r 0cba7d8f48ab ._annotateBed
Binary file ._annotateBed has changed
diff -r 000000000000 -r 0cba7d8f48ab ._annotateBedWrapper.xml
Binary file ._annotateBedWrapper.xml has changed
diff -r 000000000000 -r 0cba7d8f48ab annotateBed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annotateBed	Sun Dec 02 12:11:45 2012 -0500
@@ -0,0 +1,2 @@
+#!/bin/sh
+${0%/*}/bedtools annotate "$@"
diff -r 000000000000 -r 0cba7d8f48ab annotateBedWrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annotateBedWrapper.xml	Sun Dec 02 12:11:45 2012 -0500
@@ -0,0 +1,44 @@
+<tool id="annotateBed" name="annotateBed">
+
+    <description>TYPE_DESCRIPTION_HERE</description>
+
+    <command interpreter="bash">
+	names=""
+	inputfiles=""
+	#for $i, $s in enumerate($annotateColumn)
+		names=$names + ${s.colname} + " "
+		inputfiles=$inputfiles+ ${s.colfile} + " "
+	#end for
+	bedtools annotate $countflag -names $names -i $inputRegion -files $inputfiles
+	</command>
+
+    <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" />
+		<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" />
+		</repeat>
+
+    </inputs>
+
+    <outputs>
+
+        <data format="bed" name="output" />
+  
+    </outputs>
+
+<help>
+
+.. class:: infomark
+
+IMPORTANT INFORMATION
+
+----
+
+WRITE HELP HERE
+
+</help>
+
+</tool>
\ No newline at end of file