<tool id="getGRset" name="GRsetFromGEO">
  <description>downloads data from GEO</description>
  <requirements>
  <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
  <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
  </requirements>
  <stdio>
  <exit_code range="1:" />
  </stdio>
  <command>Rscript $__tool_directory__/GRsetFromGEO.R $input output.RData</command>
  <inputs>
    <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
  </inputs>
  <outputs>
    <data format="RDdata" name="output" label="output.RData" />
  </outputs>
  <help>
    **What it does**
    This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object
    **Input**
    The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
    **Output**
    GenomicRatioSet object
  </help>
</tool>
Rscript $__tool_directory__/GRsetFromGEO.R "$input" "$output"