<tool id="AP" name="annotatePeak" version="1.16.2">
  <requirements>
         <requirement type="package" version="3.2.1">R</requirement>
     </requirements>
<stdio>
   <exit_code range="1:" />
</stdio>
  <command> Rscript $__tool_directory__/annotatePeak.R "$DMR" "$annoPeakTable"</command>
  <inputs>
    <param optional="false" format="bed" name="DMR" type="data" value="" help="Bumphunter peaks." label="[required] file">
      <validator type="empty_field" message="This field is required."/>
    </param>
  </inputs>
  <outputs>
    <data format="csv" name="annoPeakTable" label="peakAnno.csv"/>
  </outputs>
  <tests>
    <test>
      <param name="test">
      <element name="test-data">
          <collection type="data">
          <element name="DMR" value="test-data/DMR.bed"/>
          </collection>
        </element>
        </param>
        <output format="csv" name="annoPeakTable" label="test-data/annoPeakTable.csv"/>
        </test>
    </tests>
  <help>
**Description**
</help>
<citations>
DMR
</citations>
</tool>
