view closestBed.xml @ 11:b7f1d9f8f3bc

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<tool id="closestbed" name="closestBed">
  <description>find closest features</description>
  <command>closestBed -a $inputa -b $inputb $strandness -d $no -t $tie> $output_data
  </command>
  <inputs>
      <param name="inputa" type="data" format="interval,bam,bed,gff,vcf" label="Input A (-a)"/>
      <param name="inputb" type="data" format="interval,bam,bed,gff,vcf" label="Input B (-b)"/>          
      <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>
      
    <param name="no" label="Only look for non-overlaping features" type="boolean" truevalue="-no" falsevalue="" checked="False"/>
              <param name="tie" type="select" label="Strand requirement" >
		<option value="all" selected="true"> report all ties </option>
        <option value="first" > report the first that occurred</option>
        <option value="last" > report the last that occurred </option>
      </param>
        </inputs>
  <outputs>
    <data format="input" name="output_data"/> 
  </outputs>
  <help>

**What it does**

This is a wrapper for closestBed.

  </help>
</tool>