view select_optimal_cluster.xml @ 2:7edf4d48a350 draft default tip

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<tool id="select_optimal_cluster" name="Select Optimal Cluster" version="1.0.0">
  <description> 
  Select the Optimal Clusters from TITAN
  </description>
  <requirements>
    <requirement type="binary">Rscript</requirement>
    <requirement type="package" version="3.2.1">R</requirement>
    <requirement type="package" version="1.0">cancer_genomics_functions</requirement>
    <requirement type="environment" verion="1.0">CANCER_GENOMICS_FUNCTIONS_PATH</requirement>
  </requirements>
  <command>

  Rscript $__tool_directory__/select_optimal_cluster.R
    --input_params 
    #for $f in $params:
     $f 
    #end for 
    --input_segments
    #for $f in $segments:
     $f
    #end for
    #if $method.method_selector == "validity_index"
      --method validity_index
    #else
      --method validity_index_and_pga
      -pga $method.pga
    #end if
    --output_param $output_param
    --output_segment $output_segment
    -cgfp \$CANCER_GENOMICS_FUNCTIONS_PATH

  </command>

  <inputs>
    <conditional name="method">
      <param name="method_selector" type="select" label="Method for Cluster Selection">
        <option value="validity_index" selected="True">Min Val Index</option>
        <option value="validity_index_and_pga">Min Val Index + PGA Threshold</option>
      </param>
      <when value="validity_index_and_pga">
        <param name="pga" type="float" min="0.0" max="1.0" value="0.8" label="Maximum Percent Genome Alteration"/> 
      </when>
    </conditional>
    <param type="data_collection" format="txt" collection_type="list" name="params"/>
    <param type="data_collection" format="txt" collection_type="list" name="segments"/> 
  </inputs>

  <outputs>
    <data format="txt" name="output_param" label="Optimal TITAN parameters output"/>
    <data format="txt" name="output_segment" label="Optimal TITAN segments output"/>
  </outputs>

</tool>