--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spatial_proximity.xml	Sat Mar 10 07:59:27 2012 -0500
@@ -0,0 +1,32 @@
+<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>