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15
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1 <tool id="GetGEO" name="GRsetFromGEO" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
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4 </requirements>
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5 <stdio>
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6 <exit_code range="1:" />
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7 </stdio>
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8 <command><![CDATA[
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9 Rscript $__tool_directory__/GRsetFromGEO.R -a "$input" > "$output"
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10 ]]></command>
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11 <inputs>
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12 <param type="text" name="input" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
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13 </inputs>
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14 <outputs>
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15 <data name="output" format="RDdata" label="GRsetFromGEO.RData"/>
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="input" value="GSE51547"/>
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20 <output name="output" file="test-data/out.RData"/>
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5
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21 </test>
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22 </tests>
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15
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23 <help>**What it does**
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24 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object
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25 **Input**
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26 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
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27 **Output**
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28 GenomicRatioSet object</help>
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29 <citations>
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30 <citation type="doi">10.1093/bioinformatics/btu049</citation>
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31 </citations>
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5
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32 </tool>
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