<tool id="GetGEO" name="GRsetFromGEO" version="0.1.0">
    <requirements>
        <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
      Rscript $__tool_directory__/GRsetFromGEO.R -a "$input" > "$output"
    ]]></command>
    <inputs>
        <param type="text" name="input" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
    </inputs>
    <outputs>
        <data name="output" format="RDdata" label="GRsetFromGEO.RData"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="GSE51547"/>
            <output name="output" file="test-data/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/btu049</citation>
    </citations>
</tool>