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1 <tool id="GEO" name="getGEO" version="1.16.2">
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2 <?xml version='1.0' encoding='utf-8'?>
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3 <requirements>
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4 <tool_dependency>
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5 <package name="R" version="3.2.1">
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6 <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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7 </package>
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8 </tool_dependency>
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9 </requirements>
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10 <stdio>
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11 <exit_code range="1:" />
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12 </stdio>
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13 <command> Rscript $__tool_directory__/getGEO.R "$GSMTable" "$MetaTable" "$IlmnTable" "$gmTable"</command>
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14 <inputs>
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15 <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable">
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16 <validator type="empty_field" message="This field is required."/>
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17 </param>
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18 </inputs>
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19 <outputs>
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20 <data format="csv" name="MetaTable" label="MetaData.csv"/>
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21 <data format="csv" name="IlmnTable" label="IlmnData.csv"/>
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22 <data format="csv" name="gmTable" label="gmSet.csv"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="test">
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27 <element name="test-data">
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28 <collection type="data">
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29 <element name="GSMTable" value="test-data/input.csv" />
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30 </collection>
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31 </element>
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32 </param>
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33 <output format="csv" name="MetaTable" label="test-data/MetaTable.csv"/>
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34 <output format="csv" name="IlmnTable" label="test-data/IlmnTable.csv"/>
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35 <output format="csv" name="gmTable" label="test-data/gmTable.csv"/>
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36 </test>
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37 </tests>
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38 <help>
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39 **Description**
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40 </help>
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41 <citations>
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42 GEO
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43 </citations>
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44 </tool>
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