Mercurial > repos > jay > pdaug_ml_models

annotate PDAUG_ML_Models/PDAUG_ML_Models.xml @ 6:8697dc4a7f45 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
author jay
date Sun, 31 Jan 2021 02:43:58 +0000
parents 5448f9425c6a
children
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1 <tool id="pdaug_ml_models" name="PDAUG ML Models" version="0.1.0" python_template_version="3.6">
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2 <description> Machine learning modeling </description>
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4 <requirements>
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6 <requirement type="package" version="4.10.0">plotly</requirement>
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7 <requirement type="package" version="3.6">python</requirement>
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8 <requirement type="package" version="0.25.3">pandas</requirement>
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9 <requirement type="package" version="0.22.1">scikit-learn</requirement>
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10 <requirement type="package" version="1.5.2">scipy</requirement>
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11 </requirements>
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13 <command detect_errors="exit_code"><![CDATA[
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15 python '$__tool_directory__/PDAUG_ML_Models.py' '$SelMLAlgo.MLAlgo'
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17 #if $SelMLAlgo.MLAlgo == 'SVMC'
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18 #if $SelMLAlgo.settings.advanced == "advanced"
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19 --cache_size '$SelMLAlgo.settings.cache_size'
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20 --C '$SelMLAlgo.settings.C'
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21 --kernel '$SelMLAlgo.settings.kernel'
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22 --degree '$SelMLAlgo.settings.degree'
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23 --gamma '$SelMLAlgo.settings.gamma'
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24 --coef0 '$SelMLAlgo.settings.coef0'
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25 --probability '$SelMLAlgo.settings.probability'
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26 --shrinking '$SelMLAlgo.settings.shrinking'
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27 --tol '$SelMLAlgo.settings.tol'
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28 --verbose '$SelMLAlgo.settings.verbose'
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29 --max_iter '$SelMLAlgo.settings.max_iter'
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30 --decision_function_shape '$SelMLAlgo.settings.decision_function_shape'
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31 --randomState '$SelMLAlgo.settings.randomState'
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32 --breakties '$SelMLAlgo.settings.breakties'
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33 #end if
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34 #end if
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35
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36 #if $SelMLAlgo.MLAlgo == 'SGDC'
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37 #if $SelMLAlgo.settings.advanced == "advanced"
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38 --loss '$SelMLAlgo.settings.loss'
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39 --penalty '$SelMLAlgo.settings.penalty'
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40 --alpha '$SelMLAlgo.settings.alpha'
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41 --l1_ratio '$SelMLAlgo.settings.l1_ratio'
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42 --fit_intercept '$SelMLAlgo.settings.fit_intercept'
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43 --max_iter '$SelMLAlgo.settings.max_iter'
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44 --tol '$SelMLAlgo.settings.tol'
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45 --shuffle '$SelMLAlgo.settings.shuffle'
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46 --verbose '$SelMLAlgo.settings.verbose'
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47 --epsilon '$SelMLAlgo.settings.epsilon'
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48 --n_jobs '$SelMLAlgo.settings.n_jobs'
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49 --random_state '$SelMLAlgo.settings.random_state'
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50 --learning_rate '$SelMLAlgo.settings.learning_rate'
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51 --eta0 '$SelMLAlgo.settings.eta0'
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52 --power_t '$SelMLAlgo.settings.power_t'
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53 --early_stopping '$SelMLAlgo.settings.early_stopping'
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54 --validation_fraction '$SelMLAlgo.settings.validation_fraction'
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55 --n_iter_no_change '$SelMLAlgo.settings.n_iter_no_change'
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56 --warm_start '$SelMLAlgo.settings.warm_start'
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57 --average '$SelMLAlgo.settings.average'
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58
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59 #end if
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60 #end if
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61
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62 #if $SelMLAlgo.MLAlgo == 'DTC'
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63 #if $SelMLAlgo.settings.advanced == "advanced"
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64 --criterion '$SelMLAlgo.settings.criterion'
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65 --splitter '$SelMLAlgo.settings.splitter'
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66 --max_depth '$SelMLAlgo.settings.max_depth'
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67 --min_samples_split '$SelMLAlgo.settings.min_samples_split'
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68 --min_samples_leaf '$SelMLAlgo.settings.min_samples_leaf'
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69 --min_weight_fraction_leaf '$SelMLAlgo.settings.min_weight_fraction_leaf'
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70 --max_features '$SelMLAlgo.settings.max_features'
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71 --random_state '$SelMLAlgo.settings.random_state'
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72 --max_leaf_nodes '$SelMLAlgo.settings.max_leaf_nodes'
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73 --min_impurity_decrease '$SelMLAlgo.settings.min_impurity_decrease'
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74 --min_impurity_split '$SelMLAlgo.settings.min_impurity_split'
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75 --presort '$SelMLAlgo.settings.presort'
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76 --ccpalpha '$SelMLAlgo.settings.ccpalpha'
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77 #end if
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78 #end if
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79
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80
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81 #if $SelMLAlgo.MLAlgo == 'GBC'
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82 #if $SelMLAlgo.settings.advanced == "advanced"
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83 --loss '$SelMLAlgo.settings.loss'
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84 --learning_rate '$SelMLAlgo.settings.learning_rate'
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85 --n_estimators '$SelMLAlgo.settings.n_estimators'
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86 --subsample '$SelMLAlgo.settings.subsample'
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87 --criterion '$SelMLAlgo.settings.criterion'
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88 --min_samples_split '$SelMLAlgo.settings.min_samples_split
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89 --min_samples_leaf '$SelMLAlgo.settings.min_samples_leaf''
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90 --min_weight_fraction_leaf '$SelMLAlgo.settings.min_weight_fraction_leaf'
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91 --max_depth '$SelMLAlgo.settings.max_depth'
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parents: 0
diff changeset
92 --min_impurity_decrease '$SelMLAlgo.settings.min_impurity_decrease'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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parents: 0
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93 --min_impurity_split '$SelMLAlgo.settings.min_impurity_split'
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parents: 0
diff changeset
94 --init '$SelMLAlgo.settings.init'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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parents: 0
diff changeset
95 --random_state '$SelMLAlgo.settings.random_state'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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96 --max_features '$SelMLAlgo.settings.max_features'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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parents: 0
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97 --verbose '$SelMLAlgo.settings.verbose'
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98 --max_leaf_nodes '$SelMLAlgo.settings.max_leaf_nodes'
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parents: 0
diff changeset
99 --warm_start '$SelMLAlgo.settings.warm_start'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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100 --presort '$SelMLAlgo.settings.presort'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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101 --validation_fraction '$SelMLAlgo.settings.validation_fraction'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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102 --n_iter_no_change '$SelMLAlgo.settings.n_iter_no_change'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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diff changeset
103 --tol '$SelMLAlgo.settings.tol'
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104 --ccpalpha '$SelMLAlgo.settings.ccpalpha'
0
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105 #end if
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diff changeset
106 #end if
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107
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diff changeset
108 #if $SelMLAlgo.MLAlgo == 'RFC'
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109 #if $SelMLAlgo.settings.advanced == "advanced"
1
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110 --n_estimators '$SelMLAlgo.settings.n_estimators'
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111 --criterion '$SelMLAlgo.settings.criterion'
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112 --max_depth '$SelMLAlgo.settings.max_depth'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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113 --min_samples_split '$SelMLAlgo.settings.min_samples_split'
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114 --min_samples_leaf '$SelMLAlgo.settings.min_samples_leaf'
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115 --min_weight_fraction_leaf '$SelMLAlgo.settings.min_weight_fraction_leaf'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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116 --max_features '$SelMLAlgo.settings.max_features'
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117 --max_leaf_nodes '$SelMLAlgo.settings.max_leaf_nodes'
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parents: 0
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118 --min_impurity_decrease '$SelMLAlgo.settings.min_impurity_decrease'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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119 --min_impurity_split '$SelMLAlgo.settings.min_impurity_split'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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120 --bootstrap '$SelMLAlgo.settings.bootstrap'
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121 --oob_score '$SelMLAlgo.settings.oob_score'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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122 --n_jobs '$SelMLAlgo.settings.n_jobs'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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123 --random_state '$SelMLAlgo.settings.random_state'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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124 --verbose '$SelMLAlgo.settings.verbose'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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125 --warm_start '$SelMLAlgo.settings.warm_start'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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126 --ccp_alpha '$SelMLAlgo.settings.ccp_alpha'
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127 --max_samples '$SelMLAlgo.settings.max_samples'
0
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128 #end if
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129 #end if
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130
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131
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132 #if $SelMLAlgo.MLAlgo == 'LRC'
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133 #if $SelMLAlgo.settings.advanced == "advanced"
1
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134 --penalty '$SelMLAlgo.settings.penalty'
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135 --dual '$SelMLAlgo.settings.dual'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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136 --tol '$SelMLAlgo.settings.tol'
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137 --C '$SelMLAlgo.settings.C'
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138 --fit_intercept '$SelMLAlgo.settings.fit_intercept'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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139 --intercept_scaling '$SelMLAlgo.settings.intercept_scaling'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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140 --random_state '$SelMLAlgo.settings.random_state'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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141 --solver '$SelMLAlgo.settings.solver'
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142 --max_iter '$SelMLAlgo.settings.max_iter'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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143 --multi_class '$SelMLAlgo.settings.multi_class'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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144 --verbose '$SelMLAlgo.settings.verbose'
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145 --warm_start '$SelMLAlgo.settings.warm_start'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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146 --n_jobs '$SelMLAlgo.settings.n_jobs'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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147 --l1_ratio '$SelMLAlgo.settings.l1_ratio'
0
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148 #end if
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149 #end if
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150
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151 #if $SelMLAlgo.MLAlgo == 'KNC'
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152 #if $SelMLAlgo.settings.advanced == "advanced"
1
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153 --n_neighbors '$SelMLAlgo.settings.n_neighbors'
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154 --weights '$SelMLAlgo.settings.weights'
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155 --algorithm '$SelMLAlgo.settings.algorithm'
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156 --leaf_size '$SelMLAlgo.settings.leaf_size'
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157 --p '$SelMLAlgo.settings.p'
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158 --metric '$SelMLAlgo.settings.metric'
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159 --n_jobs '$SelMLAlgo.settings.n_jobs'
0
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160 #end if
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161 #end if
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162
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163 #if $SelMLAlgo.MLAlgo == 'GNBC'
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164 #if $SelMLAlgo.settings.advanced == "advanced"
1
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165 --var_smoothing '$SelMLAlgo.settings.var_smoothing'
0
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166 #end if
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167 #end if
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168
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169 #if $SelMLAlgo.MLAlgo == 'MLP'
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170 #if $SelMLAlgo.settings.advanced == "advanced"
1
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171 --hidden_layer_sizes '$SelMLAlgo.settings.hidden_layer_sizes'
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172 --activation '$SelMLAlgo.settings.activation'
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173 --solver '$SelMLAlgo.settings.solver'
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174 --alpha '$SelMLAlgo.settings.alpha'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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175 --batch_size '$SelMLAlgo.settings.batch_size'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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176 --learning_rate '$SelMLAlgo.settings.learning_rate'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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177 --learning_rate_init '$SelMLAlgo.settings.learning_rate_init'
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178 --power_t '$SelMLAlgo.settings.power_t'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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179 --max_iter '$SelMLAlgo.settings.max_iter'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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180 --shuffle '$SelMLAlgo.settings.shuffle'
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181 --random_state '$SelMLAlgo.settings.random_state'
5448f9425c6a "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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182 --tol '$SelMLAlgo.settings.tol'
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183 --verbose '$SelMLAlgo.settings.verbose'
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184 --warm_start '$SelMLAlgo.settings.warm_start'
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185 --momentum '$SelMLAlgo.settings.momentum'
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186 --nesterovs_momentum '$SelMLAlgo.settings.nesterovs_momentum'
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187 --early_stopping '$SelMLAlgo.settings.early_stopping'
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188 --validation_fraction '$SelMLAlgo.settings.validation_fraction'
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189 --beta_1 '$SelMLAlgo.settings.beta_1'
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190 --beta_2 '$SelMLAlgo.settings.beta_2'
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191 --epsilon '$SelMLAlgo.settings.epsilon'
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192 --n_iter_no_change '$SelMLAlgo.settings.n_iter_no_change'
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193 --max_fun '$SelMLAlgo.settings.max_fun'
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194 --TrainFile '$SelMLAlgo.settings.TrainFile'
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195 --TestMethod '$SelMLAlgo.settings.TestMethod'
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196 --SelectedSclaer '$SelMLAlgo.settings.SelectedSclaer'
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197 --NFolds '$SelMLAlgo.settings.NFolds'
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198 --Testspt '$SelMLAlgo.settings.Testspt'
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199 --TestFile '$SelMLAlgo.settings.TestFile'
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200 --OutFile '$SelMLAlgo.settings.OutFile'
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201 --htmlOutDir '$SelMLAlgo.settings.htmlOutDir'
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202 --htmlFname '$SelMLAlgo.settings.htmlFname'
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203 --Workdirpath '$SelMLAlgo.settings.Workdirpath'
0
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204 #end if
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205 #end if
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206
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207 --TrainFile '$input1' --TestMethod '$TestMethods.SelTestMethods' --SelectedSclaer '$scalling'
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208 --htmlOutDir '$output2.extra_files_path'
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209
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210 --htmlFname '$output2'
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211
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212 --OutFile '$output1'
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213
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214 #if $TestMethods.SelTestMethods == 'predict'
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215 --TestFile '$TestMethods.input2'
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216 #end if
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217
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218 #if $TestMethods.SelTestMethods == 'Internal'
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219 --NFolds '$TestMethods.nFolds'
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220 #end if
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221 ]]></command>
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222
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223 <inputs>
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224
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225 <param name="input1" label="Input file" type="data" format="tabular" argument= "--TrainFile"/>
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226
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227 <conditional name='SelMLAlgo' >
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228
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229 <param name="MLAlgo" type="select" label="Machine learning algorithms" argument="">
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230 <option value="SVMC">SVMC</option>
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231 <option value="SGDC">SGDC</option>
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232 <option value="DTC">DTC</option>
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233 <option value="GBC">GBC</option>
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234 <option value="RFC">RFC</option>
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235 <option value="LRC">LRC</option>
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236 <option value="KNC">KNC</option>
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237 <option value="GNBC">GNBC</option>
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238 <option value="MLP">MLP</option>
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239 </param>
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240
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241 <when value="SVMC">
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242 <conditional name="settings">
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243 <param name="advanced" type="select" label="Select advanced parameters">
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244 <option value="simple" selected="true">No, use program defaults.</option>
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245 <option value="advanced">Yes, see full parameter list.</option>
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246 </param>
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247 <when value="simple">
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248
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249 </when>
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250
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251 <when value="advanced">
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252 <param name="C" type="float" label="Regularization parameter" value="1.0" help="Regularization parameter. For details(https://scikit-learn.org/stable/modules/generated/sklearn.svm.SVC.html)" argument="--C"/>
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253 <param name="kernel" type="select" label="Kernel" argument="" help="Specifies the kernel type to be used in the algorithm.">
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254 <option value="rbf">rbf</option>
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255 <option value="poly">poly</option>
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256 <option value="linear">linear</option>
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257 <option value="sigmoid">sigmoid </option>
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258 </param>
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259 <param name="degree" type="integer" label="degree" value="3" help="degree" />
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260 <param name="gamma" type="text" label="gamma" value="scale" help="gamma" />
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261 <param name="coef0" type="float" label="coef0" value="0.0" help="coef0" />
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262 <param name="shrinking" type="boolean" label="shrinking" value="true" help="shrinking" />
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263 <param name="probability" type="boolean" label="probability" value="true" help="probability" />
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264 <param name="tol" type="float" label="tol" value="1e-3" help="tol" />
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265 <param name="verbose" type="boolean" label="verbose" value="false" help="verbose" />
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266 <param name="max_iter" type="integer" label="max_iter" value="-1" help="max_iter" />
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267 <param name="decision_function_shape" type="select" label="decision_function_shape" argument="" help="Decision Function Shape">
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268 <option value="ovo">ovo</option>
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269 <option value="ovr">ovr</option>
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270 </param>
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271 <param name="randomState" type="integer" label="randomState" value="100" help="Random State)" />
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272 <param name="breakties" type="boolean" label="breakties" value="false" help="Break ties" />
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273 <param name="cache_size" type="float" label="cache_size" value="100" help="Cache size" />
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274 </when>
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275 </conditional>
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276 </when>
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277
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278 <when value="SGDC">
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279 <conditional name="settings">
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280 <param name="advanced" type="select" label="Specify advanced parameters">
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281 <option value="simple" selected="true">No, use program defaults.</option>
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282 <option value="advanced">Yes, see full parameter list.</option>
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283 </param>
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284 <when value="simple">
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285 </when>
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286
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287 <when value="advanced">
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288 <param name="loss" type="select" label="loss" argument="" help="--loss" >
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289 <option value="hinge" > hinge</option>
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290 <option value="log" selected="true" > log </option>
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291 <option value="modified_huber" > modified_huber </option>
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292 <option value="squared_hinger" > squared_hinger </option>
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293 <option value="perceptron" > perceptron </option>
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294 </param>
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295 <param name="penalty" type="select" label="penalty" argument="" help="--penalty" >
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296 <option value="l2" selected="true"> l2 </option>
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297 <option value="l1"> l1 </option>
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298 <option value="elasticnet" > elasticnet </option>
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299 </param>
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300 <param name="alpha" type="float" label="alpha" value="0.0001" help="--alpha" />
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301 <param name="l1_ratio" type="float" label="l1_ratio" value="0.15" help="--l1_ratio" />
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302 <param name="fit_intercept" type="boolean" label="fit_intercept" value="true" help="--fit_intercept" />
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303 <param name="max_iter" type="integer" label="max_iter" value="1000" help="--max_iter" />
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304 <param name="tol" type="float" label="tol" value="1e-3" help="--tol" />
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305 <param name="shuffle" type="boolean" label="shuffle" value='true' help="--shuffle" />
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306 <param name="verbose" type="integer" label="verbose" value="0" help="--verbose" />
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307 <param name="epsilon" type="float" label="epsilon" value="0.1" help="--epsilon" />
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308 <param name="n_jobs" type="text" label="n_jobs" value="none" help="--n_jobs" />
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309 <param name="random_state" type="text" label="random_state" value="none" help="--random_state" />
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310 <param name="learning_rate" type="select" label="learning_rate" argument="" help="--learning_rate" >
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311 <option value="constant" selected="true" > constant </option>
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312 <option value="optimal" > optimal </option>
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313 <option value="invscaling"> invscaling </option>
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314 <option value="adaptive"> adaptive </option>
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315 </param>
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316 <param name="eta0" type="float" label="eta0" value="1e-3" help="--eta0" />
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317 <param name="power_t" type="float" label="power_t" value="0.5" help="--power_t" />
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318 <param name="early_stopping" type="boolean" label="early_stopping" value="false" help="--early_stopping" />
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319 <param name="validation_fraction" type="float" label="validation_fraction" value="0.1" help="--validation_fraction" />
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320 <param name="n_iter_no_change" type="integer" label="n_iter_no_change" value="5" help="--n_iter_no_change" />
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321 <param name="warm_start" type="boolean" label="warm_start" value='false' help="--warm_start" />
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322 <param name="average" type="boolean" label="average" value="false" help="--average" />
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323 </when>
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324 </conditional>
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325 </when>
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326
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327 <when value="DTC">
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328 <conditional name="settings">
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329 <param name="advanced" type="select" label="Specify advanced parameters">
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330 <option value="simple" selected="true">No, use program defaults.</option>
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331 <option value="advanced">Yes, see full parameter list.</option>
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332 </param>
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333 <when value="simple">
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334 </when>
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335
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336 <when value="advanced">
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337 <param name="criterion" type="select" label="criterion" argument="" help="--criterion" >
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338 <option value="gini" selected="true" > gini </option>
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339 <option value="entropy"> entropy </option>
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340 </param>
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341 <param name="splitter" type="select" label="splitter" argument="" help="--splitter" >
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342 <option value="best" selected="true" > best </option>
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343 <option value="random"> random </option>
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344 </param>
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345 <param name="max_depth" type="integer" label="10" value="10" help="--max_depth" />
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346 <param name="min_samples_split" type="float" label="min_samples_split" value="2" help="--min_samples_split" />
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347 <param name="min_samples_leaf" type="float" label="min_weight_fraction_leaf" value="1" help="--min_weight_fraction_leaf" />
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348 <param name="min_weight_fraction_leaf" type="float" label="min_weight_fraction_leaf" value="0.0" help="--min_weight_fraction_leaf" />
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349 <param name="max_features" type="text" label="max_features" value='none' help="--max_features" >
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350 </param>
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351 <param name="random_state" type="integer" label="random_state" value="10" help="--random_state" />
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352 <param name="max_leaf_nodes" type="integer" label="max_leaf_nodes" value="0" help="--max_leaf_nodes" />
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353 <param name="min_impurity_decrease" type="float" label="min_impurity_decrease" value="0.0" help="--min_impurity_decrease" />
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354 <param name="min_impurity_split" type="float" label="min_impurity_split" value="1e-7" help="--min_impurity_split" />
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355 <param name="presort" type="text" label="presort" value="deprecated" help="--presort" />
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356 <param name="ccpalpha" type="float" label="ccpalpha" value="0.0" help="--ccpalpha" />
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357 </when>
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358 </conditional>
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359 </when>
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360
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361 <when value="GBC">
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362 <conditional name="settings">
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363 <param name="advanced" type="select" label="Specify advanced parameters">
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364 <option value="simple" selected="true">No, use program defaults.</option>
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365 <option value="advanced">Yes, see full parameter list.</option>
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366 </param>
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367 <when value="simple">
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368 </when>
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369
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370 <when value="advanced">
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371 <param name="loss" type="select" label="loss" argument="" help="loss" >
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372 <option value="simple" selected="true" > simple </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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diff changeset
373 <option value="advanced">advanced</option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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diff changeset
374 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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diff changeset
375 <param name="learning_rate" type="float" label="learning_rate" value="0.1" help="--learning_rate" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
376 <param name="n_estimators" type="integer" label="n_estimators" value="100" help="--n_estimators" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
377 <param name="subsample" type="float" label="subsample" value="1.0" help="--subsample" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
378 <param name="criterion" type="select" label="criterion" argument="" help="--criterion" >
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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diff changeset
379 <option value="mse" selected="true">mse</option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
380 <option value="friedman_mse">friedman_mse</option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
381 <option value="mae" > mae </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
382 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
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diff changeset
383 <param name="min_samples_split" type="text" label="min_samples_split" value="2" help="--min_samples_split" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
384 <param name="min_samples_leaf" type="text" label="min_samples_leaf" value="1" help="--min_samples_leaf" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
385 <param name="min_weight_fraction_leaf" type="float" label="min_weight_fraction_leaf" value="0.0" help="--min_weight_fraction_leaf" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
386 <param name="max_depth" type="integer" label="max_depth" value="3" help="--max_depth" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
387 <param name="min_impurity_decrease" type="float" label="min_impurity_decrease" value="0.0" help="--min_impurity_decrease" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
388 <param name="min_impurity_split" type="float" label="min_impurity_split" value="1e-7" help="--min_impurity_split" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
389 <param name="init" type="select" label="init" argument="" help="init" >
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
390 <option value="none" selected="true">None</option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
391 <option value="Zero">Zero</option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
392 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
393 <param name="random_state" type="text" label="random_state" value="none" help="--random_state"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
394 <param name="max_features" type="text" label="max_features" value="none" help="--max_features" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
395 <param name="verbose" type="integer" label="verbose" value="0" help="--verbose" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
396 <param name="max_leaf_nodes" type="text" label="max_leaf_nodes" value="none" help="--max_leaf_nodes" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
397 <param name="warm_start" type="boolean" label="warm_start" value='false' help="--warm_start" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
398 <param name="presort" type="text" label="presort" value="deprecated" help="--presort" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
399 <param name="validation_fraction" type="float" label="validation_fraction" value="0.1" help="--validation_fraction" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
400 <param name="n_iter_no_change" type="text" label="n_iter_no_change" value="none" help="--n_iter_no_change" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
401 <param name="tol" type="float" label="tol" value="1e-4" help="--tol" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
402 <param name="ccpalpha" type="float" label="ccpalpha" value="0.0" help="--ccpalpha" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
403 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
404 </conditional>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
405 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
406
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
407 <when value="RFC">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
408 <conditional name="settings">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
409 <param name="advanced" type="select" label="Specify advanced parameters">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
410 <option value="simple" selected="true">No, use program defaults.</option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
411 <option value="advanced">Yes, see full parameter list.</option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
412 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
413 <when value="simple">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
414 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
415 <when value="advanced">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
416 <param name="n_estimators" type="integer" label="n_estimators" value="100" help="--n_estimators" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
417 <param name="criterion" type="select" label="criterion" argument="" help="--criterion" >
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
418 <option value="gini" selected="true"> gini </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
419 <option value="entropy">entropy</option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
420 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
421 <param name="max_depth" type="text" label="max_depth" value="none" help="--max_depth" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
422 <param name="min_samples_split" type="text" label="min_samples_split" value="2" help="--min_impurity_split" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
423 <param name="min_samples_leaf" type="text" label="min_samples_leaf" value="1" help="--min_samples_leaf" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
424 <param name="min_weight_fraction_leaf" type="float" label="min_weight_fraction_leaf" value="0" help="--min_weight_fraction_leaf" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
425 <param name="max_features" type="text" label="max_features" value='auto' help="--max_features" >
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
426
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
427 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
428 <param name="max_leaf_nodes" type="text" label="max_leaf_nodes" value="none" help="--max_leaf_nodes" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
429 <param name="min_impurity_decrease" type="float" label="min_impurity_decrease" value="0" help="--min_impurity_decrease" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
430 <param name="min_impurity_split" type="float" label="min_impurity_split" value="1e-7" help="--min_impurity_split" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
431 <param name="bootstrap" type="boolean" label="bootstrap" value="true" help="--bootstrap" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
432 <param name="oob_score" type="boolean" label="oob_score" value="false" help="--oob_score" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
433 <param name="n_jobs" type="text" label="n_jobs" value="none" help="--n_jobs" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
434 <param name="random_state" type="text" label="random_state" value="none" help="--random_state" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
435 <param name="verbose" type="integer" label="verbose" value="0" help="--verbose" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
436 <param name="warm_start" type="boolean" label="warm_start" help="--warm_start" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
437 <param name="ccp_alpha" type="float" label="ccp_alpha" value="0.0" help="--ccp_alpha" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
438 <param name="max_samples" type="text" label="max_samples" value="none" help="--max_samples" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
439 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
440 </conditional>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
441 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
442
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
443 <when value="LRC">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
444 <conditional name="settings">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
445 <param name="advanced" type="select" label="Specify advanced parameters">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
446 <option value="simple" selected="true">No, use program defaults.</option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
447 <option value="advanced">Yes, see full parameter list.</option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
448 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
449 <when value="simple">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
450 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
451 <when value="advanced">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
452 <param name="penalty" type="select" label="fit_intercept" argument="" help="--fit_intercept" >
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
453 <option value="l2" selected="true"> l1 </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
454 <option value="l1" > l2 </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
455 <option value="elastic" > elastic </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
456 <option value="None" > None </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
457 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
458 <param name="dual" type="boolean" label="dual" value="false" help="--dual" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
459 <param name="tol" type="float" label="tol" value="1e-4" help="--tol" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
460 <param name="C" type="float" label="C" value="1.0" help="--C" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
461 <param name="fit_intercept" type="boolean" label="fit_intercept" value="true" help="--fit_intercept" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
462 <param name="intercept_scaling" type="float" label="intercept_scaling" value="1.0" help="intercept_scaling" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
463 <param name="random_state" type="text" label="random_state" value="none" help="--random_state" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
464 <param name="solver" type="select" label="solver" argument="" help="--solver" >
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
465 <option value="newton-cg" > newton-cg </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
466 <option value="lbfgs" selected="true" > lbfgs </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
467 <option value="saga" > saga </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
468 <option value="sag" > sag </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
469 <option value="liblinear" >liblinear </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
470 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
471 <param name="max_iter" type="integer" label="max_iter" value="100" help="--max_iter" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
472 <param name="multi_class" type="select" label="multi_class" argument="" help="--multi_class" >
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
473 <option value="auto" selected="true" > auto </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
474 <option value="ovr" > ovr </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
475 <option value="multinomial" > multinomial </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
476 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
477 <param name="verbose" type="integer" label="verbose" value="0" help="--verbose" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
478 <param name="warm_start" type="boolean" label="warm_start" value="false" help="--warm_start" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
479 <param name="n_jobs" type="text" label="n_jobs" value="none" help="--n_jobs" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
480 <param name="l1_ratio" type="text" label="l1_ratio" value="none" help="--l1_ratio" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
481 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
482 </conditional>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
483 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
484
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
485 <when value="KNC">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
486 <conditional name="settings">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
487 <param name="advanced" type="select" label="Specify advanced parameters">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
488 <option value="simple" selected="true">No, use program defaults.</option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
489 <option value="advanced">Yes, see full parameter list.</option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
490 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
491
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
492 <when value="simple">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
493 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
494
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
495 <when value="advanced">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
496 <param name="n_neighbors" type="integer" value="5" label="Number of neighbors to use" argument="--n_neighbors" help="Number of neighbors to use" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
497 <param name="weights" type="select" label="Weight function" argument="--weights" help="weight function used in prediction. Possible values:" >
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
498 <option value="uniform" selected="true" > Uniform </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
499 <option value="distance" > Distance </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
500 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
501 <param name="p" type="integer" label="Power parameter" value="2" help="Power parameter for the Minkowski metric." />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
502 <param name="leaf_size" type="integer" label="Leaf size" value="30" argument="--leaf_size" help="Leaf size passed to BallTree or KDTree." />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
503 <param name="algorithm" type="select" label="solver" argument="" help="--solver" >
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
504 <option value="ball_tree" > BallTree </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
505 <option value="kd_tree" > KDTree </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
506 <option value="brute"> Brute-Force </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
507 <option value="auto" selected="true"> Auto</option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
508 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
509 <param name="metric" type="select" label="Distance metric" help="The distance metric to use for the tree." >
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
510 <option value="minkowski" selected="true"> Minkowski </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
511 <option value="precomputed" >Precomputed </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
512 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
513 <param name="n_jobs" type="integer" label="N-jobs" value="-1" help="The number of parallel jobs to run for neighbors search" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
514 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
515 </conditional>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
516
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
517 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
518
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
519 <when value="GNBC">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
520 <conditional name="settings">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
521 <param name="advanced" type="select" label="Specify advanced parameters">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
522 <option value="simple" selected="true">No, use program defaults.</option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
523 <option value="advanced">Yes, see full parameter list.</option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
524 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
525 <when value="simple">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
526 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
527 <when value="advanced">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
528 <param name="var_smoothing" type="float" label="var_smoothing" value="1e-9" help="--var_smoothing" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
529 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
530 </conditional>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
531 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
532
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
533 <when value="MLP">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
534 <conditional name="settings">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
535 <param name="advanced" type="select" label="Specify advanced parameters">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
536 <option value="simple" selected="true">No, use program defaults.</option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
537 <option value="advanced">Yes, see full parameter list.</option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
538 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
539 <when value="simple">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
540 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
541 <when value="advanced">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
542 <param name="hidden_layer_sizes" type="text" label="hidden_layer_sizes" value="100," help="--hidden_layer_sizes" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
543 <param name="activation" type='select' label="activation" help="--hidden_layer_sizes" >
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
544 <option value="indentity" > indentity </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
545 <option value="logistic" > logistic </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
546 <option value="tanh" > tanh </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
547 <option value="relu" selected="true" > relu </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
548 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
549
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
550 <param name="solver" type="select" label="solver" help="--solver" >
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
551 <option value="lbfgs" > lbfgs </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
552 <option value="sgd" > sgd </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
553 <option value="adam" selected="true" >adam </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
554 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
555
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
556 <param name="alpha" type="float" value="0.0001" label="alpha" help="--alpha" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
557 <param name="batch_size" type="text" value="auto" label="batch_size" help="--batch_size" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
558 <param name="learning_rate" type="select" label="learning_rate" help="--learning_rate" >
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
559 <option value="constant" selected="true" >constant </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
560 <option value="invscaling" >invscaling </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
561 <option value="adaptive" >adaptive </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
562 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
563 <param name="learning_rate_int" type="float" value="0.001" label="learning_rate_int" help="--learning_rate_int" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
564 <param name="power_t" type="float" value="0.5" label="power_t" help="--power_t" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
565 <param name="max_iter" type="integer" value="200" label="max_iter" help="--max_iter" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
566 <param name="shuffle" type="boolean" label="shuffle" value="true" help="--shuffle" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
567 <param name="random_state" type="text" label="random_state" value="none" help="--random_state" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
568 <param name="tol" type="float" label="tol" value="1e-4" help="--tol" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
569 <param name="verbose" type="boolean" label="verbose" value="false" help="--verbose" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
570 <param name="warm_start" type="boolean" label="warm_start" value="false" help="--warm_start" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
571 <param name="momentum" type="float" label="momentum" value="0.9" help="--momentum" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
572 <param name="nesterovs_momentum" type="boolean" label="nesterovs_momentum" value="true" help="--nesterovs_momentum" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
573 <param name="early_stopping" type="boolean" label="early_stopping" value="false" help="--early_stopping" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
574 <param name="validation_fraction" type="float" label="validation_fraction" value="0.1" help="--validation_fraction" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
575 <param name="beta_1" type="float" label="beta_1" value="0.9" help="--beta_1" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
576 <param name="beta_2" type="float" label="beta_1" value="0.999" help="--beta_2" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
577 <param name="epsilon" type="float" label="epsilon" value="1e-8" help="--epsilon" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
578 <param name="n_iter_no_change" type="integer" label="n_iter_no_change" value="10" help="--n_iter_no_change" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
579 <param name="max_fun" type="integer" label="max_fun" value="15000" help="--max_fun" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
580 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
581 </conditional>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
582 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
583
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
584 </conditional>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
585
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
586 <conditional name='TestMethods'>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
587 <param name="SelTestMethods" type="select" label="Choose the Test method" argument="--TestMethod" help="Data testing method">
6
8697dc4a7f45 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents: 1
diff changeset
588 <option value="Internal">Internal Test</option>
8697dc4a7f45 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents: 1
diff changeset
589 <option value="TestSplit">Train Test Split</option>
8697dc4a7f45 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents: 1
diff changeset
590 <option value="External">External Test Data</option>
8697dc4a7f45 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents: 1
diff changeset
591 <option value="Predict">Predict Unknown</option>
0
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
592 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
593 <when value="Internal">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
594 <param name="nFolds" type="integer" label="Cross validation" value="5" min="5" max="10" argument="--nfold" help="Cross validation"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
595 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
596 <when value="TestSplit">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
597 <param name="TestSplit" type="float" label="Split Training data" value="0.2" min="0.0" max="1.0" argument="-X" help="Split Training data"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
598 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
599 <when value="External">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
600 <param name="input2" type="data" label="Test data file" format="tabular" argument="--TestFile" help="Tabular file with text data"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
601 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
602 <when value="Predict">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
603 <param name="input2" type="data" format="Unlabeled data file" argument="--TestFile" help="Unlabeled data for predict"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
604 </when>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
605 </conditional>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
606
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
607 <param name="scalling" type="select" label="Data scalling options" argument="--SelectScaler" help="Data scalling options">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
608 <option value="Min_Max"> Min_Max </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
609 <option value="Standard_Scaler"> Standard_Scaler </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
610 <option value="No_Scaler"> No_Scaler </option>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
611 </param>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
612 </inputs>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
613
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
614 <outputs>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
615 <data name='output1' format='tabular' label="${tool.name} on $on_string - ${SelMLAlgo.MLAlgo} (tabular)" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
616 <data name='output2' format='html' label="${tool.name} on $on_string - ${SelMLAlgo.MLAlgo} (webpage)" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
617 </outputs>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
618
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
619
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
620 <tests>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
621
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
622 <test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
623 <param name="input1" value="test.tsv"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
624 <param name="MLAlgo" value="SVMC" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
625 <param name="scalling" value="Min_Max"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
626 <output name="output1" file="test1/report_dir/SVMC.tsv" lines_diff="2"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
627 <output name="output2" file="test1/report_dir/SVMC.html" lines_diff="2" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
628 </test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
629
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
630 <test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
631 <param name="input1" value="test.tsv"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
632 <param name="MLAlgo" value="GNBC" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
633 <param name="scalling" value="Min_Max"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
634 <output name="output1" file="test2/GNBC.tsv" lines_diff='2'/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
635 <output name="output2" file="test2/report_dir/GNBC.html" lines_diff='2'/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
636 </test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
637
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
638 <test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
639 <param name="input1" value="test.tsv"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
640 <param name="MLAlgo" value="SGDC" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
641 <param name="scalling" value="Min_Max"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
642 <output name="output1" file="test3/SGDC.tsv" lines_diff='2'/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
643 <output name="output2" file="test3/report_dir/SGDC.html" lines_diff='2'/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
644 </test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
645
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
646 <test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
647 <param name="input1" value="test.tsv"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
648 <param name="MLAlgo" value="DTC" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
649 <param name="scalling" value="Min_Max"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
650 <output name="output1" file="test4/DTC.tsv" lines_diff='2' />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
651 <output name="output2" file="test4/report_dir/DTC.html" lines_diff='2'/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
652 </test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
653
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
654 <test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
655 <param name="input1" value="test.tsv"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
656 <param name="MLAlgo" value="GBC" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
657 <param name="scalling" value="Min_Max"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
658 <output name="output1" file="test5/GBC.tsv" lines_diff='2' />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
659 <output name="output2" file="test5/report_dir/GBC.html" lines_diff='2'/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
660 </test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
661
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
662 <test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
663 <param name="input1" value="test.tsv"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
diff changeset
664 <param name="MLAlgo" value="RFC" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
665 <param name="scalling" value="Min_Max"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
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666 <output name="output1" file="test6/RFC.tsv" lines_diff='2' />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
667 <output name="output2" file="test6/report_dir/RFC.html" lines_diff='2'/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
diff changeset
668 </test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
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669
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
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670 <test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
diff changeset
671 <param name="input1" value="test.tsv"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
672 <param name="MLAlgo" value="LRC" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
673 <param name="scalling" value="Min_Max"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
674 <output name="output1" file="test7/LRC.tsv" lines_diff='2' />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
675 <output name="output2" file="test7/report_dir/LRC.html" lines_diff='2'/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
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676 </test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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677
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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678 <test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
679 <param name="input1" value="test.tsv"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
diff changeset
680 <param name="MLAlgo" value="KNC" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
681 <param name="scalling" value="Min_Max"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
682 <output name="output1" file="test8/KNC.tsv" lines_diff='2'/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
683 <output name="output2" file="test8/report_dir/KNC.html" lines_diff='2'/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
diff changeset
684 </test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
diff changeset
685
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
686 <test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
687 <param name="input1" value="test.tsv"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
688 <param name="MLAlgo" value="MLP" />
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
689 <param name="scalling" value="Min_Max"/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
690 <output name="output1" file="test9/MLP.tsv" lines_diff='2'/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
691 <output name="output2" file="test9/report_dir/MLP.html" lines_diff='2'/>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
692 </test>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
diff changeset
693
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
694 </tests>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
695
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
696
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
697
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
698 <help><![CDATA[
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
699 .. class:: infomark
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
diff changeset
700
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
701 **What it does**
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
702
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
703 This tool builds a machine learning model from the given descriptor set based on the binary class label. There are 8 different machine learning algorithms that have been implemented up to 10 fold cross-validation. We have also implemented standard scaler and MinMaxScaler normalization. 
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
704
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
705 * **Support Vector Machine Classifier**
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
706 * **Stochastic gradient descent Classifier**
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
707 * **Decision tree**
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
708 * **Gradient boosting Classifier**
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
709 * **Random Forest Classifier**
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
710 * **Logistic regression Classifier**
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
711 * **k-nearest neighbors Classifier**
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
712 * **Gaussian naive Bayes Classifier**
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
713 * **Multilayer perceptron Classifier**
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
714
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
715 A detail Description of all the algorithms can be found at sklearn (https://scikit-learn.org/stable/)
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
716
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
717 -----
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
718
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
719 **Inputs**
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
720 * **Training File** Tabulalr files with labeled peptide descriptor data.
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
721 * **Select Machine Learning algorithms** Select algorithm.
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
722 * **Select Advanced Parameters** Select the advance parameter details of each of the parameters that can be found on sklearn website. 
6
8697dc4a7f45 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents: 1
diff changeset
723 * **Select the test method** (Internal Test, Train Test Split, External Test Data, and Predict Unknown)
0
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
724 * **Cross Validation** Up to 10 fold cross-validation.
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
725 * **Method to Scale the data** MinMaxScaler and standard scaler.
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
726
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
727 -----
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
728
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
729 **Outputs**
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
730 * Tabular file with the various performance scores (accurracy, precision, recall, f1-score, and AUC score). ]]></help>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
731
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
732 <citations>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
733 <citation type="bibtex">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
734 @misc{PDAUGGITHUB,
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
735 author = {Joshi, Jayadev and Blankenberg, Daniel},
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
736 year = {2020},
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
737 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
738 publisher = {GitHub},
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
739 journal = {GitHub repository},
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
740 url =
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
741 {https://github.com/jaidevjoshi83/pdaug.git},
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
742
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
743 }</citation>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
744
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
745 <citation type="bibtex">
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
746 @article{scikit-learn,
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
747 title={Scikit-learn: Machine Learning in {P}ython},
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
748 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
749 and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
750 and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
751 Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
752 journal={Journal of Machine Learning Research},
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
753 volume={12},
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
754 pages={2825--2830},
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
755 year={2011}
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
756 }</citation>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
757 </citations>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
758 </tool>
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
759
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
760
0973f093d98f "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
761