view segToMatrix.xml @ 54:59dbe857f5d4

introduce normal_CNV parameter

<tool id="segToMatrix" name="segToMatrix" version="0.0.1">
  <description>
    Prepare segmented copy number data for Xena
  </description>
  <command interpreter="python">
    seg2matrix/segToMatrixGalaxy.py $input $__tool_directory__/seg2matrix/$refGene.assembly $outputMatrix $outputProbeMap $normal_CNV_value
  </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>
    <param name="normal_CNV_value" type="text" value="0" lable="what is the value to represent normal copy number" />
  </inputs>
  <outputs>
    <data name="outputMatrix" format="tabular" label="xena copy number matrix" />
    <data name="outputProbeMap" format="tabular" label="associated probemap"/>
  </outputs>
  <help>

**Given a segmented copy number data file, convert it into xena ready matrix file.**

1. Input data file format: tab-deliminated

   =======    =====  ======= ===== ====== ======
   sanmple    chr    start   end   strand value
   =======    =====  ======= ===== ====== ======
   sample1    chr1   1       100   .      0.5
   sample2    chr1   101     1000  .      1.5
   sample3    chr1   1000    2000  .      -0.5
   ...        ...    ...     ...   ...    ...
   =======    =====  ======= ===== ====== ====== 


2. Output File no 1. matrix file

   Output File no 2. probeMap file -- probe to gene mapping file  (is in the same genome assembly as the input segmented copy number data)
  </help>
</tool>