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1 <tool id="aggreg" name="aggregation" version="1.0.0">
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2 <description>predict phenotype by combining multiple classifiers</description>
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3 <command interpreter="Rscript">
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4 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 <param name="lassoPred" type="data" optional="true"
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9 label="lasso prediction" help="path to rds containing LASSO prediction"
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10 />
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11
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12 <param name="rfPred" type="data" optional="true"
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13 label="rf prediction" help="path to rds containing Random Forest prediction"
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14 />
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15
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16 <param name="rrBLUPPred" type="data" optional="true"
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17 label="rrBLUP prediction" help="path to rds containing rrBLUP prediction"
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18 />
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19
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20 <param name="svmPred" type="data" optional="true"
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21 label="SVM prediction" help="path to rds containing SVM prediction"
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22 />
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23
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24 <param name="phenotype" type="data"
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25 label="phenotype data" help=" a tabular datatype containing the phenotypes "
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26 />
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27
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28 <param name="eval" type="integer" value="0"
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29 label="do evaluation" help=" whether to produce a model or to use folds to evaluate the tool. 1 means the tool will be evaluate (and a folds argument is required) any other value produces a model "
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30 />
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31
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32 <param name="folds" type="data" optional="true"
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33 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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34 />
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35
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36 <param name="model" type="data" optional="true"
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37 label="model" help= " a path to a file where the results (depending on the chosen mode) will be writen"
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38 />
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39 <!-- deprecated <param name="out" type="text"
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40 label="output path" help= " a path to a rds file" -->
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41 />
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42 <param name="method" type="text" value="svm"
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43 label="aggregation method" help= "choose among geneticMean, rrBLUP, lasso, rf or svm"
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44 />
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45 <param name="kernel" type="text" value="linear"
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46 label="kernel for SVM" help= "choose among linear, polynomial, radial, sigmoid"
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47 />
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48
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49 </inputs>
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50
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51 <configfiles>
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52 <configfile name="config">
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53 ## Desc: this file is sourced in encode wrapper script
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54 ## as means to pass all galaxy params to R
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55 "${lassoPred}" -> lassoPred
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56 "${rfPred}" -> rfPred
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57 "${rrBLUPPred}" -> rrBLUPPred
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58 "${svmPred}" -> svmPred
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59 "${phenotype}" -> phenotype
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60 "${model}" -> model
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61 "${output1}" -> out
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62 "${eval}" -> evaluation
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63 "${folds}" -> folds
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64 "${method}" -> method
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65 "${kernel}" -> kernel
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66 "${eval}" -> doEvaluation
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67
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68 </configfile>
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69 </configfiles>
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70
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71 <outputs>
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72 <data format="tabular" name = "output1" label="aggregation output" />
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73 </outputs>
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74
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75 <help>
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76
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77 </help>
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78 </tool> |
