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31
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1 <tool id="GEO" name="getGEO" version="1.16.2">
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2 <requirements>
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3 <requirement type="package" version="3.2.1">R</requirement>
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4 </requirements>
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32
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5 <stdio>
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33
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6 <exit_code> range="1:" level="fatal" </exit_code>
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32
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7 </stdio>
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31
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8 <command> Rscript $__tool_directory__/getGEO.R "$GSMTable" "$MetaTable" "$IlmnTable" "$gmTable"</command>
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9 <inputs>
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10 <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable">
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11 <validator type="empty_field" message="This field is required."/>
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12 </param>
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13 </inputs>
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14 <outputs>
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15 <data format="csv" name="MetaTable" label="MetaData.csv"/>
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16 <data format="csv" name="IlmnTable" label="IlmnData.csv"/>
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17 <data format="csv" name="gmTable" label="gmSet.csv"/>
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="test">
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22 <element name="test-data">
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23 <collection type="data">
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24 <element name="GSMTable" value="test-data/input.csv" />
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25 </collection>
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26 </element>
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27 </param>
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28 <output format="csv" name="MetaTable" label="test-data/MetaTable.csv"/>
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29 <output format="csv" name="IlmnTable" label="test-data/IlmnTable.csv"/>
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30 <output format="csv" name="gmTable" label="test-data/gmTable.csv"/>
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31 </test>
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32 </tests>
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33 <help>
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34 **Description**
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35 </help>
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36 <citations>
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37 GEO
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38 </citations>
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39 </tool>
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