--- a/spatial_proximity.xml	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-<tool id="spatialproximity" name="spatial proximity">
-  <description>of two interval sets</description>
-  <command interpreter="python">spatial_proximity.py $inputa $inputb $genome  $outplot $outlog $outbed $strandness
-  </command>
-  <inputs>
-    <param name="inputa" format="interval" type="data" label="Interval set 1" />
-    <param name="inputb" format="interval" type="data" label="Interval set 2" />
-    <param name="genome" type="select" label="Select genome">
-     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option>
-     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option>
-     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option>
-     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option>
-    </param>
-          <param name="strandness" type="select" label="Strand requirement" >
-		<option value="" selected="true"> none </option>
-        <option value="-s" > -s: closest feature on the same strand</option>
-        <option value="-S" > -S: closest feature on the opposite strand </option>
-      </param>
-  </inputs>
-  <outputs>
-    <data format="input" name="outbed" label="${tool.name} on ${on_string}: (bed)" />
-    <data format="pdf" name="outplot" label="${tool.name} on ${on_string}: (plot)" />
-      <data format="txt" name="outlog" label="${tool.name} on ${on_string}: (log)" />
-  </outputs>
-  <help>
-  
-.. class:: infomark
-
-for each feature in the first interval set, find the closest in the second set, then compared the distance distribution to shuffled set 1.
-
-  </help>
-</tool>