view GEO/getGEO.xml @ 34:6025fa3bfc40 draft

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<tool id="GEO" name="getGEO" version="1.16.2">
  <requirements>
         <requirement type="package" version="3.2.1">R</requirement>
     </requirements>
     <stdio>
         <exit_code> range="1:" level="fatal" </exit_code>
     </stdio>
  <command> Rscript $__tool_directory__/getGEO.R "$GSMTable" "$MetaTable" "$IlmnTable" "$gmTable"</command>
  <inputs>
    <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable">
      <validator> type="empty_field" message="This field is required."</validator>
    </param>
  </inputs>
  <outputs>
    <data> format="csv" name="MetaTable" label="MetaData.csv" </data>
    <data> format="csv" name="IlmnTable" label="IlmnData.csv"</data>
    <data> format="csv" name="gmTable" label="gmSet.csv"</data>
  </outputs>
  <tests>
    <test>
      <param name="test">
      <element name="test-data">
          <collection type="data">
              <element name="GSMTable" value="test-data/input.csv" />
          </collection>
        </element>
        </param>
        <output format="csv" name="MetaTable" label="test-data/MetaTable.csv"/>
        <output format="csv" name="IlmnTable" label="test-data/IlmnTable.csv"/>
        <output format="csv" name="gmTable" label="test-data/gmTable.csv"/>
        </test>
    </tests>
  <help>
**Description**
</help>
<citations>
GEO
</citations>
</tool>