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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="getGRsetFromGEO" name="getGRsetFromGEO" version="1.18.4">
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3 <requirements>
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4 <requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
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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 $__tool_directory__/getGRsetFromGEO.R "$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="RDdata" name="output" label="getGRsetFromGEO.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 type="data" format="RData" name="output" label="test-data/out.RData"/>
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26 </test>
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27 </tests>
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28 <help>
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29 **What it does**
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30 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object
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31 **Input**
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32 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
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33 **Output**
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34 GenomicRatioSet object
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35 </help>
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36 <citations>
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37 <citation type="doi">10.1093/bioinformatics/btu049</citation>
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38 </citations>
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39 </tool>
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