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1 <tool id="GEO" name="getGEO" version="1.16.2">
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14
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2 <macros>
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3 <import>getGEO_macros.xml</import>
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4 </macros>
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5 <expand macro="requirements" />
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11
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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 $__tool_directory__/getGEO.R "$GSMTable" "$MetaTable" "$IlmnTable" "$gmTable"</command>
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10 <inputs>
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11 <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable">
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12 <validator type="empty_field" message="This field is required."/>
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13 </param>
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14 </inputs>
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15 <outputs>
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16 <data format="csv" name="MetaTable" label="MetaData.csv"/>
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17 <data format="csv" name="IlmnTable" label="IlmnData.csv"/>
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18 <data format="csv" name="gmTable" label="gmSet.csv"/>
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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="GSMTable" value="test-data/input.csv" />
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26 </collection>
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27 </element>
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28 </param>
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29 <output format="csv" name="MetaTable" label="test-data/MetaTable.csv"/>
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30 <output format="csv" name="IlmnTable" label="test-data/IlmnTable.csv"/>
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31 <output format="csv" name="gmTable" label="test-data/gmTable.csv"/>
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32 </test>
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33 </tests>
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34 <help>
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35 **Description**
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36 </help>
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37 <citations>
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38 GEO
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39 </citations>
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40 </tool>
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