--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mytools/bedclean.xml	Tue Mar 13 23:34:52 2012 -0400
@@ -0,0 +1,33 @@
+<tool id="bedclean" name="clean interval">
+  <description>remove off-chromosome lines</description>
+  <command interpreter="python">bedclean.py $input $genome $output > $log  </command>
+  <inputs>
+     <param name="input" type="data" format="interval" label="Original interval file"/>
+    <param name="genome" type="select" label="Select genome">
+     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option>
+     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option>
+     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option>
+     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="input" name="output" label="${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
+
+
+  </help>
+</tool>