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1 <tool id="GRset" name="GRsetFromGEO" version="1.16.2">
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27
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2 <description>
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3 Reading Illumina methylation array data from GEO.
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4 </description>
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5 <requirements>
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27
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6 <requirement type="package" version="3.2.1">R</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" />
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10 </stdio>
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11 <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command>
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12 <inputs>
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27
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13 <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/>
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12
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14 </inputs>
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15 <outputs>
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16 <data format="RData" name="output" label="GenomicRatioSet.RData"/>
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="test">
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21 <element name="test-data">
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22 <collection type="data">
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23 <element name="GSE" value="GSE51547"/>
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24 </collection>
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25 </element>
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26 </param>
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27 <output format="RData" name="output" label="test-data/GenomicRatioSet.RData"/>
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28 </test>
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29 </tests>
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30 <help>
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31 Reading Illumina methylation array data from GEO.
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32 </help>
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33 <citations>
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34 Aryee, Martin J, et al "Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays" Bioinformatics 3010 (2014): 1363-1369
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35 </citations>
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36 </tool>
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