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1 <tool id="aggregEval" name="aggregation_evaluation" version="1.0.0">
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2 <description>tool to evaluate aggregation accuracy</description>
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3 <command interpreter="Rscript">
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4 evaluate_aggregation.R $config > ${output1}
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5 </command>
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6
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7 <inputs>
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8
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9 <param name="genotype" type="data"
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10 label="genotype data" help="path to a file containing the encoded genotypes"
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11 />
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12
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13 <param name="lasso" type="data" optional="true"
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14 label="lasso model" help="path to rds containing LASSO model"
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15 />
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16
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17 <param name="rf" type="data" optional="true"
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18 label="rf model" help="path to rds containing Random Forest model"
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19 />
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20
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21 <param name="rrBLUP" type="data" optional="true"
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22 label="rrBLUP model" help="path to rds containing rrBLUP model"
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23 />
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24
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25 <param name="svm" type="data" optional="true"
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26 label="SVM model" help="path to rds containing SVM model"
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27 />
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28
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29 <param name="phenotype" type="data"
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30 label="phenotype data" help=" a tabular datatype containing the phenotypes "
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31 />
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32
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33 <param name="folds" type="data"
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34 label="folds" help=" OPTIONAL ARGUMENT path to a folds file containing folds indexes in a R list called /folds/ such as produced by the folds tools in OGHMA suite. "
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35 />
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36 <param name="method" type="text" value="svm"
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37 label="aggregation method" help= "choose among geneticMean, dt, lasso, rf or svm"
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38 />
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39 <param name="kernel" type="text" value="linear"
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40 label="kernel for SVM" help= "choose among linear, polynomial, radial, sigmoid"
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41 />
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42
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43 </inputs>
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44
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45 <configfiles>
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46 <configfile name="config">
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47 ## Desc: this file is sourced in encode wrapper script
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48 ## as means to pass all galaxy params to R
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49 "${genotype}" -> genotype
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50 "${lasso}" -> lassoModel
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51 "${rf}" -> rfModel
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52 "${rrBLUP}" -> rrBLUPModel
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53 "${svm}" -> svmModel
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54 "${phenotype}" -> phenotype
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55 "${output1}" -> out
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56 "${folds}" -> folds
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57 "${method}" -> method
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58 "${kernel}" -> kernel
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59
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60 </configfile>
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61 </configfiles>
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62
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63 <outputs>
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64 <data format="tabular" name = "output1" label="aggregation evaluation" />
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65 </outputs>
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66
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67 <help>
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68
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69 </help>
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70 </tool> |
