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1 <tool id="getGRset" name="GRsetFromGEO">
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2 <description>downloads data from GEO</description>
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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 <requirement type="package" version="0.6.0">bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command>Rscript $__tool_directory__/GRsetFromGEO.R $input output.rdata</command>
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11 <inputs>
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12 <param format="text" name="input" type="text" 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 format="rdata" name="output" label="output.rdata" />
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16 </outputs>
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17 <help>
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18 **What it does**
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19 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object
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20 **Input**
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21 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
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22 **Output**
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23 GenomicRatioSet object
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24 </help>
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25 </tool>
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26 Rscript $__tool_directory__/GRsetFromGEO.R "$input" "$output"
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