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<?xml version="1.0" encoding="UTF-8"?>
<tool id="findDMR" name="findDMR" version="1.20.0">
<requirements>
<requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
</requirements>
<stdio>
<exit_code range="1:" />
</stdio>
  <command> Rscript $__tool_directory__/findDMR.R "$input1" "$input2" "$cutoff" "$B"  "$pickCutoffQ" "$output1"  "$output2"</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'"/>
    <param name="cutoff" type="text" value="0.5" label="Cutoff" help="A  v. Values of the estimate of the genomic profile above the cutoff or below the negative of the cutoff will be used as candidate regions. It is possible to give two separate values (upper and lower bounds). If one value is given, the lower bound is minus the value."/>
     <param name="B" type="text" value="0" label="Number of resamples" help="An integer denoting the number of resamples to use when computing null distributions. This defaults to 0. If permutations is supplied that defines the number of permutations/bootstraps and B is ignored."/>
     <param name="pickCutoffQ" type="text" value="0.99" label="pickCutoffQ" help="The quantile used for picking the cutoff using the permutation distribution."/>
  </inputs>
  <outputs>
    <data format="text" type="data" name="output1" label="DMR.txt"/>
    <data format="bed" type="data" name="output2" label="DMR.bed"/>
  </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 name="input2" type="data" format="csv" label="test-data/OLDvsYOUNG.csv"/>
                <element name="cutoff" value="0.5"/>
                <element name="B" value="0"/>
                <element name="pickCutoffQ" value="0.99"/>
          </collection>
        </element>
        </param>
        <output name="output1" type="data" format="text" label="test-data/DMR.txt"/>
        <output name="output2" type="data" format="bed" label="test-data/DMR.bed"/>
        </test>
    </tests>
  <help>
**What it does**
This R-based tool look for genomic regions that are differentially methylated between two conditions
**Input**
GenomicRatioSet object
**Output**
Text and BED file containing differentially methylated regions
  </help>
  <citations>
<citation type="doi">10.1093/bioinformatics/btu049</citation>
  </citations>
</tool>