--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bed_clean.xml	Sat Mar 31 13:08:38 2012 -0400
@@ -0,0 +1,37 @@
+<tool id="bed_clean" name="bed_clean">
+  <description>clean up BED files</description>
+  <command interpreter="python">bed_clean.py $input $genome $output > $log  </command>
+  <inputs>
+     <param name="input" type="data" format="interval" label="Original interval file"/>
+
+            <param name="genome" type="select" label="Select chromsome size file" >
+                <options from_file="chrsize.loc">
+                    <column name="name" index="0"/>
+                    <column name="value" index="1"/>
+                </options>
+            </param>
+
+  </inputs>
+  <outputs>
+    <data format="input" name="output" label="${tool.name} on ${on_string} (interval)"/>
+    <data format="txt" name="log" label="${tool.name} on ${on_string} (log)"/>
+  </outputs>
+  <help>
+
+**Description**
+
+remove lines that are
+
+1. comment or track name lines
+
+2. on chr*_random
+
+3. or have negative coordinates
+
+4. or the end is larger than chromosome size
+
+5. convert strand * to + 
+
+
+  </help>
+</tool>