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1 <tool id="GRset" name="GRsetFromGEO" version="1.16.2">
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2 <requirements>
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3 <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</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> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command>
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9 <inputs>
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10 <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
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11 </inputs>
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12 <outputs>
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13 <data format="Rdata" name="output" label="GenomicRatioSet.Rdata"/>
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14 </outputs>
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15 <tests>
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16 <test>
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17 <param name="test">
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18 <element name="test-data">
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19 <collection type="data">
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20 <element name="GSE" value="GSE51547"/>
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21 </collection>
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22 </element>
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23 </param>
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24 <output format="Rdata" name="output" label="test-data/GenomicRatioSet.Rdata"/>
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25 </test>
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26 </tests>
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27 <help>
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28 Reading Illumina methylation array data from GEO.
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29 </help>
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30 <citations>
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31 Aryee, Martin J., et al. "Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays." Bioinformatics 30.10 (2014): 1363-1369.
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32 </citations>
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33 </tool>
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