view segToGeneMatrix.xml @ 40:72dc9215623d

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<tool id="segToGeneMatrix" name="segToGeneMatrix" version="0.0.1">
  <description>
    Convert segmented copy number data to gene-level matrix data
  </description>
  <command interpreter="python">
    seg2matrix/mapSegToGeneMatrix.py $input $__tool_directory__/seg2matrix/$refGene.assembly $outputMatrix
  </command>
  <inputs>
    <param name="input" format="tabular" type="data" multiple="false" label="Input segmented copy number data" />
    <conditional name="refGene">
      <param name="assembly_select" type="select" label="Which human genome assembly is your input segmented copy number data?">
	<option value="hg19">hg19</option>
	<option value="hg18">hg18</option>
      </param>
      <when value="hg19">
        <param name="assembly" type="hidden" value="refGene_hg19" />
      </when>
      <when value="hg18">
        <param name="assembly" type="hidden" value="refGene_hg18" />
      </when>
    </conditional>  
  </inputs>
  <outputs>
    <data name="outputMatrix" format="tabular" label="gene-level copy number matrix" />
  </outputs>
  <help>

    **Given a segmented copy number data file, convert it into gene-level matrix data, also xena ready**

    Output File no 1. matrix file

  </help>
</tool>