<tool id="DMR" name="findDMR" version="1.16.2">
  <requirements>
         <requirement type="package" version="3.2.1">R</requirement>
     </requirements>
<stdio>
   <exit_code range="1:" />
</stdio>
  <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$IlmnTable" "$gmTable" "$cutoff" "$clusterSize" "$DMR"</command>
  <inputs>
    <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GSM ID and phenotype table." label="[required] GSMTable">
      <validator type="empty_field" message="This field is required."/>
    </param>
     <param optional="false" format="csv" name="IlmnTable" type="data" value="" help="CG, CHR, BP table." label="[required] IlmnTable">
      <validator type="empty_field" message="This field is required."/>
    </param>
     <param optional="false" format="csv" name="gmTable" type="data" value="" help="gmSet of data." label="[required] gmTable">
      <validator type="empty_field" message="This field is required."/>
    </param>
    <param name="cutoff" type="float" value=""
	       label="Enter cutoff size (number)"
	       help="e.g. '0.2'" >
      </param>
    <param name="clusterSize" type="float" value=""
	       label="Enter cluster size (number)"
	       help="e.g. '2'" >
      </param>
  </inputs>
  <outputs>
    <data format="bed" name="DMR" label="DMR.bed"/>
  </outputs>
  <tests>
    <test>
      <param name="test">
      <element name="test-data">
          <collection type="data">
              <element name="GSMTable" value="test-data/input.csv"/>
              <element name="IlmnTable" value="test-data/IlmnTable.csv"/>
              <element name="gmTable" value="test-data/gmTable.csv"/>
              <element name="cutoff" value="0.2"/>
              <element name="clusterSize" value="2"/>
          </collection>
        </element>
        </param>
        <output format="bed" name="DMR" label="test-data/DMR.bed"/>
        </test>
    </tests>
  <help>
**Description**
</help>
<citations>
DMR
</citations>
</tool>