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1 <tool id="select_optimal_cluster" name="Select Optimal Cluster" version="1.0.0">
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2 <description>
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3 Select the Optimal Clusters from TITAN
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4 </description>
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5 <requirements>
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6 <requirement type="binary">Rscript</requirement>
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7 <requirement type="package" version="3.2.1">R</requirement>
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8 <requirement type="package" version="1.0">cancer_genomics_functions</requirement>
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9 <requirement type="environment" verion="1.0">CANCER_GENOMICS_FUNCTIONS_PATH</requirement>
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10 </requirements>
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11 <command>
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12
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13 Rscript $__tool_directory__/select_optimal_cluster.R
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14 --input_params
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15 #for $f in $params:
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16 $f
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17 #end for
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18 --input_segments
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19 #for $f in $segments:
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20 $f
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21 #end for
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22 #if $method.method_selector == "validity_index"
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23 --method validity_index
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24 #else
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25 --method validity_index_and_pga
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26 -pga $method.pga
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27 #end if
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28 --output_param $output_param
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29 --output_segment $output_segment
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30 -cgfp \$CANCER_GENOMICS_FUNCTIONS_PATH
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31
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32 </command>
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33
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34 <inputs>
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35 <conditional name="method">
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36 <param name="method_selector" type="select" label="Method for Cluster Selection">
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37 <option value="validity_index" selected="True">Min Val Index</option>
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38 <option value="validity_index_and_pga">Min Val Index + PGA Threshold</option>
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39 </param>
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40 <when value="validity_index_and_pga">
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41 <param name="pga" type="float" min="0.0" max="1.0" value="0.8" label="Maximum Percent Genome Alteration"/>
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42 </when>
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43 </conditional>
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44 <param type="data_collection" format="txt" collection_type="list" name="params"/>
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45 <param type="data_collection" format="txt" collection_type="list" name="segments"/>
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46 </inputs>
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47
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48 <outputs>
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49 <data format="txt" name="output_param" label="Optimal TITAN parameters output"/>
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50 <data format="txt" name="output_segment" label="Optimal TITAN segments output"/>
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51 </outputs>
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52
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53 </tool>
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