<tool id="GRset" name="GRsetFromGEO" version="1.16.2">
  <description>
   Reading Illumina methylation array data from GEO.
  </description>
  <requirements>
         <requirement type="package" version="3.2.1">R</requirement>
     </requirements>
<stdio>
   <exit_code range="1:" />
</stdio>
  <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command>
  <inputs>
     <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
  </inputs>
  <outputs>
   <data format="txt" name="output" label="GenomicRatioSet.txt"/>
  </outputs>
  <tests>
    <test>
      <param name="test">
      <element name="test-data">
          <collection type="data">
                <element name="GSE" value="GSE51547"/>
          </collection>
        </element>
        </param>
        <output format="txt" name="output" label="test-data/GenomicRatioSet.txt"/>
        </test>
    </tests>
  <help>
Reading Illumina methylation array data from GEO.
</help>
<citations>
Aryee, Martin J, et al "Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays" Bioinformatics 3010 (2014): 1363-1369
</citations>
</tool>