<tool id="GRset" name="GRsetFromGEO" version="1.16.2">
  <requirements>
   <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement>
   <requirement name="minfi" type="package" version="1.20.2">minfi</requirement>
   <requirement name="libcurl" type="package" version="7.35">libcurl</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="Rdata" name="output" label="GenomicRatioSet.Rdata"/>
  </outputs>
  <tests>
    <test>
      <param name="test">
      <element name="test-data">
           <collection type="data">
                <element name="GSE" value="GSE51547"/>
          </collection>
        </element>
        </param>
        <output format="Rdata" name="output" label="test-data/GenomicRatioSet.Rdata"/>
        </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 30.10 (2014): 1363-1369.
</citations>
</tool>