<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>
