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1 <tool id="svm" name="svm" version="1.0.0">
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2 <description>predict phenotype using a SVM approach</description>
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3 <command interpreter="Rscript">
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4 svm.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="genotype" type="data"
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9 label="genotype data" help="a tabular datatype containing the encoded genotypes"
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10 />
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11
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12 <param name="phenotype" type="data"
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13 label="phenotype data" help=" a tabular datatype containing the phenotypes "
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14 />
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15
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16 <param name="kernel" type="text" value="radial"
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17 label="name of the kernel" help= " four possibilities : radial, linear, polynomial or sigmoid. Any other value is treated as radial"
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18 />
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19
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20 <param name="cost" type="float" value="-1"
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21 label="cost" help="the cost parameter of SVM used by all kernels. Suitable values are between 0.1 and 1000. -1 means the parameter must be optimized by the tool "
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22 />
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23
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24 <param name="gamma" type="float" value="-1"
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25 label="gamma" help="the gamma parameter of SVM used by radial, polynomial and sigmoid kernels. Suitable values are between 1e-06 and 1. -1 means the parameter must be optimized by the tool "
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26 />
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27
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28 <param name="coeficient" type="float" value="-1"
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29 label="coeficient" help="the coeficient parameter of SVM used by polynomial kernel. Suitable values are between 0 and 4. -1 means the parameter must be optimized by the tool "
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30 />
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31
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32 <param name="degree" type="float" value="-1"
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33 label="degree" help="the maximum dgree of the polynomial kernel. Suitable values are between 1 and 3. -1 means the parameter must be optimized by the tool "
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34 />
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35
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36 <param name="eval" type="integer" value="0"
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37 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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38 />
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39
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40 <param name="folds" type="data" optional="true"
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41 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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42 />
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43
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44 <!-- <param name="model" type="text"
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45 label="path to the output folds" help= " a path to a file where the results (depending on the chosen mode) will be writen"
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46 /> -->
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47 </inputs>
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48
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49 <configfiles>
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50 <configfile name="config">
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51 ## Desc: this file is sourced in encode wrapper script
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52 ## as means to pass all galaxy params to R
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53 "${genotype}" -> genotype
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54 "${phenotype}" -> phenotype
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55 "${eval}" -> doEvaluation
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56 "${folds}" -> folds
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57 "${output1}" -> out
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58 "${kernel}" -> kernel
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59 "${gamma}" -> g
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60 "${cost}" -> c
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61 "${coeficient}" -> coef
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62 "${degree}" -> d
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63
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64 </configfile>
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65 </configfiles>
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66
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67 <outputs>
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68 <data format="tabular" name = "output1" label="SVM output" />
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69 </outputs>
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70
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71 <help>
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72 make the classification using the SVM method
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73 </help>
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74 </tool> |
