<?xml version="1.0" encoding="UTF-8"?>
<tool id="findDMP" name="findDMP" version="1.20.0">
<requirements>
<requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
</requirements>
<stdio>
<exit_code range="1:" />
</stdio>
  <command> Rscript $__tool_directory__/findDMP.R "$input1" "$input2" "$output" </command>
  <inputs>
     <param format="RDdata" name="input1" type="data" label="Genomic Ratio Set" help="e.g. 'GRsetFromGEO tool output'"/>
     <param format="csv" name="input2" type="data" label="Phenotype Table"
  help="e.g.'ID Phenotype
  GSM1255789       OLD
  GSM1255798       OLD
  GSM1255778      YOUNG'"/>
  </inputs>
  <outputs>
    <data format="text" type="data" name="output" label="DMP.txt"/>
  </outputs>
  <tests>
    <test>
      <param name="test">
      <element name="test-data">
          <collection type="data">
                <element name="input1" type="data" format="RData" label="test-data/out.RData"> </element>
                <element name="input2" type="data" format="csv" label="test-data/OLDvsYOUNG.csv"> </element>
          </collection>
        </element>
        </param>
        <output name="output" type="data" format="text" label="test-data/DMP.txt"/>
        </test>
    </tests>
  <help>
**What it does**
Tool finds differentially methylated positions (DMPs) with respect to a phenotype covariate
**Input**
GenomicRatioSet object
Phenotype Table
**Output**
Text file containing differentially methylated positions
  </help>
  <citations>
<citation type="doi">10.1093/bioinformatics/btu049</citation>
  </citations>
</tool>