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12
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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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22
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4 <requirement name="minfi" type="package" version="1.16.0">minfi</requirement>
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12
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command>
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10 <inputs>
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11 <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
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12 </inputs>
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13 <outputs>
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14 <data format="Rdata" name="output" label="GenomicRatioSet.Rdata"/>
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15 </outputs>
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16 <tests>
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17 <test>
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18 <param name="test">
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19 <element name="test-data">
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20 <collection type="data">
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21 <element name="GSE" value="GSE51547"/>
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22 </collection>
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23 </element>
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24 </param>
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25 <output format="Rdata" name="output" label="test-data/GenomicRatioSet.Rdata"/>
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26 </test>
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27 </tests>
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28 <help>
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29 Reading Illumina methylation array data from GEO.
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30 </help>
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31 <citations>
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32 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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33 </citations>
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34 </tool>
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