<tool id="getGRset" name="GRsetFromGEO" version="1.0.0">
    <description>downloads data from GEO</description>
    <requirements>
        <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
        <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
    </requirements>
    <command detect_errors="aggressive">
        Rscript '$__tool_directory__/GRsetFromGEO.R' '$input' '$output'
    </command>
    <inputs>
        <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE42752'"/>
    </inputs>
    <outputs>
        <data format="rdata" name="output" label="output.rdata" />
    </outputs>
    <tests>
       <test>
           <param name="input" value="GSE42752"/>
           <output name="output" file="out.rdata"/>
       </test>
   </tests>
   <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>
   <citations>
   <citation type="doi">10.1093/bioinformatics/btm254</citation>
   <citation type="doi">10.1093/bioinformatics/btu049</citation>
   </citations>
</tool>