--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mytools/collapseBed.xml	Fri Mar 09 20:01:43 2012 -0500
@@ -0,0 +1,19 @@
+<tool id="collapseBed" name="collapse">
+  <description>intervals</description>
+  <command interpreter="python">collapseBed2.py $input $strand $score > $outfile </command>
+  <inputs>
+    <param name="input" format="interval" type="data" label="Original file"/>
+    <param name="strand" size="10" type="integer" value="6" label="strand column" help="set 0 to ignore strand information" />
+    <param name="score" size="10" type="integer" value="5" label="for duplicate lines, keep the one with max value in column" help="set 0 to ignore score information" />
+    </inputs>
+  <outputs>
+    <data format="input" name="outfile" />
+  </outputs>
+  <help>
+
+**What it does**
+
+This tool collapses genomic intervals that have the same position (and strandness if specified) and output a set of unique intervals.  
+
+  </help>
+</tool>