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1 <tool id="GRset" name="GRsetFromGEO" version="1.16.2">
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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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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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13 <param optional="false" format="txt" name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'">
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14 <validator type="empty_field" message="This field is required."/>
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15 </param>
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16 </inputs>
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17 <outputs>
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18 <data format="rdata" name="output" label="GRsetFromGEO.rdata"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="test">
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23 <element name="test-data">
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24 <collection type="data">
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25 <element name="GSE" value="GSE51547"/>
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26 </collection>
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27 </element>
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28 </param>
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36
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29 <output format="rdata" name="output" label="test-data/out.rdata"/>
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34
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30 </test>
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31 </tests>
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32 <help>
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33 **Reading Illumina methylation array data from GEO**
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34 </help>
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35 <citations>
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36 DMR
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37 </citations>
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38 </tool>
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