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1 <tool id="featureSelectR" name="Feature Selection" >
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2 <description>
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3 This tool used for extract best feature subsets cantaining input data for model building.
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4 </description>
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5 <!--command interpreter="bash">step3run.sh $file1 $model $output1 2>/dev/null </command-->
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6 <requirements>
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7 <requirement type="set_environment">FEATURE_SELECTION_R</requirement>
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11
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8 <requirement type="set_environment">R_ROOT_DIR</requirement>
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9 <requirement type="package" version="3.2.0">R</requirement>
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10 <requirement type="package" version="1.0.0">caret-tools</requirement>
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11 </requirements>
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8
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12 <command interpreter="Rscript">feature_selection.R $input $profile $finalset $function1 $resampling $repeat $number $corcutoff $SAMPLING $cores> /dev/null 2>&1 </command>
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13
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14 <inputs>
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15 <param name="input" type="data" label="Select input data file" help="input .RData file" />
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16 <param name="SAMPLING" type="select" label="Select Sampling Method for imbalanced data" help="Defualt is with No sampling. you may choose downsample or upsample" >
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17 <option value="garBage" selected="true">No Sampling</option>
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18 <option value="downsampling">downsample</option>
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19 <option value="upsampling">upsample</option>
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20 </param>
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21 <param name="function1" type="select" display="radio" label="Select appropriate function for algorithm" >
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22 <option value="rfFuncs" selected="true">random forest based function </option>
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23 <option value="lmFuncs">linear model based function</option>
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24 <option value="treebagFuncs">treebag(CART) based function</option>
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25 <option value="nbFuncs">neive bayes based function</option>
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26 </param>
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27
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28 <param name="cores" type="select" label="Set Number of Cores " help="default is 1">
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29 <option value="1" selected="true">1</option>
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30 <option value="4">4</option>
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31 <option value="8">8</option>
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32 <option value="10">10</option>
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33 <option value="16">16</option>
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34 </param>
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35
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36
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37 <param name="corcutoff" type="float" value= "0.8" min="0.0" max = "1.0" label="Select correlation cutoff" help="values bewteen 0-1. fileds above cufoff value removed from data " />
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38 <param name="resampling" type="select" label="Select appropriate resampling method" >
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39 <option value="repeatedcv" selected="true">repeatedcv </option>
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40 <option value="boot">boot</option>
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41 <option value="cv">cv</option>
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42 <option value="boot632">boot632</option>
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43 </param>
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44 <param name="repeat" type="select" label="Set Number of times to repeat" help="default is 3 ">
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45 <option value="3" selected="true">3</option>
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46 <option value="5">5</option>
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47 <option value="7">7</option>
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48 <option value="10">10</option>
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49 </param>
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50 <param name="number" type="select" label="Set Number of times Resample" help="default is 10">
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51 <option value="10" selected="true">10</option>
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52 <option value="5">5</option>
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53 <option value="15">15</option>
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54 <option value="20">20</option>
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55 <option value="25">25</option>
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56 </param>
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57
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58 </inputs>
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59 <outputs>
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60 <data type="data" format="data" name="profile" label="$function1-profile" />
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61 <data type= "data" format="data" name="finalset" label="Selected_feature.RData "/>
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62 </outputs>
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63 <help>
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64 .. class:: infomark
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65
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66 **RFE based feature selection for classification and regression**
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67
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68 Input file must be RData file obtained by converting csv file in to RData.
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69
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70 output "Selected_feature.RData" file used for model building purpose.While profile
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71
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72 represents feature selection model.
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73
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74 Correlation cutoff value is desired for choosing independent variables For example
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75
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76 Cutoff value = 0.8 removes all descriptors sharing equal or highet correlation values.
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77
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78 User may choose varous resampling methods in combination with repeats and times of resample.
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79
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80
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81
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82 </help>
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83
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84
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85 <tests>
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86 <test>
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87 <param name="input" value="testinput.RData"/>
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88 <param name="function1" value="rfFuncs" />
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89 <param name="corcutoff" value="0.6" />
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90 <param name="resampling" value="repeatedcv" />
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91 <param name="repeat" value="1" />
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92 <param name="number" value="5" />
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93 <param name="SAMPLING" value="garb" />
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94 <param name="cores" value="1" />
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95 <output name="profile" file="rfprofile.RData" compare="sim_size" delta="2000000" />
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96 <output name="finalset" file="selected_fet.RData" compare="sim_size" delta="2000000"/>
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97 </test>
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98 </tests>
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99
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100
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101 </tool>
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