<tool id="getGRset" name="GRsetFromGEO">
    <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. 'GSE51547'"/>
    </inputs>
    <outputs>
        <data format="rdata" 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>
