--- a/bedclean.xml	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-<tool id="bedclean" name="clean interval">
-  <description>remove off-chromosome lines</description>
-  <command interpreter="python">bedClean.py $input $genome $output > $log  </command>
-  <inputs>
-     <param name="input" type="data" format="interval" label="Original interval file"/>
-    <param name="genome" type="select" label="Select genome">
-     <option value="/media/data/Research/Project/galaxy/data/chrsize/mouse.mm9.genome" selected="true">mm9</option>
-     <option value="/media/data/Research/Project/galaxy/data/chrsize/mouse.mm8.genome">mm8</option>
-     <option value="/media/data/Research/Project/galaxy/data/chrsize/human.hg18.genome">hg18</option>
-     <option value="/media/data/Research/Project/galaxy/data/chrsize/human.hg19.genome">hg19</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="input" name="output" label="${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>