<tool id="findDMR" name="findDMR" version="1.16.2">
  <requirements>
   <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement>
</requirements>
<stdio>
   <exit_code range="1:" />
</stdio>
  <command> Rscript $__tool_directory__/findDMR.R "$input1" "$input2" "$output" </command>
  <inputs>
    <param name="input1" type="data" format="Rdata" label="GenomicRatioSet.Rdata" help="e.g. 'GSE51547'"/>
    <param name="input2" type="data" format="txt" label="PhenoTab.txt" help="ID and Phenotype table"/>
  </inputs>
  <outputs>
    <data format="txt" name="output" label="findDMR.txt"/>
  </outputs>
  <tests>
    <test>
      <param name="test">
      <element name="test-data"/>
           <collection type="data">
                <element format="Rdata" name="input1" label="test-data/GenomicRatioSet.Rdata"/>
                <element format="txt" name="input2" label="test-data/PhenoTab.txt"/>
          </collection>
        </param>
        <output format="txt" name="output" label="test-data/findDMR.txt"/>
        </test>
    </tests>
  <help>
Identify CpGs where methylation is associated with a continuous or categorical phenotype.
</help>
<citations>
Aryee, Martin J., et al. "Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays." Bioinformatics 30.10 (2014): 1363-1369.
</citations>
</tool>