view segToGeneMatrix.xml @ 57:eef100efcc4c

fix

<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 $normal_CNV_value
  </command>
  <inputs>
    <param name="input" format="tabular" type="data" multiple="false" label="Input segmented copy number data" help="See input data format section for required input format" />
    <conditional name="refGene">
      <param name="assembly_select" type="select" label="Which human genome assembly is your input segmented copy number data?" help="Copy number segments will be map to RefGenes of the selected assembly.">
	<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="gene-level copy number matrix" />
  </outputs>
  <help>

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

1. Input data file format: tab-deliminated

   =======    =====  ======= ===== ====== ======
   sample     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: gene-level matrix file

  </help>
</tool>