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1 <tool id="getGRset" name="GRsetFromGEO" version="1.0.0">
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60
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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 <command detect_errors="aggressive">
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8 Rscript '$__tool_directory__/GRsetFromGEO.R' '$input' '$output'
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9 </command>
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10 <inputs>
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11 <param format="text" name="input" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE42752'"/>
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60
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12 </inputs>
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13 <outputs>
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14 <data format="rdata" name="output" label="output.rdata" />
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15 </outputs>
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61
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16 <tests>
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17 <test>
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18 <param name="input" value="GSE42752"/>
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19 <output name="output" file="out.rdata"/>
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20 </test>
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21 </tests>
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22 <help>
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23 **What it does**
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24
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25 This R-based tool downloads data from GEO using getGEO from the GEOquery package and then returns a GenomicRatioSet object
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26
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27 **Input**
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28 The GSE ID of the dataset to be downloaded from GEO "e.g. 'GSE51547'"
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29
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30 **Output**
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31 GenomicRatioSet object
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32 </help>
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33 <citations>
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34 <citation type="doi">10.1093/bioinformatics/btm254</citation>
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35 <citation type="doi">10.1093/bioinformatics/btu049</citation>
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36 </citations>
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5
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37 </tool>
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