annotate main_macros.xml @ 23:75bcb7c19fcf draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
author bgruening
date Sun, 30 Dec 2018 02:00:37 -0500
parents 56ddc98c484e
children 5552eda109bd
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1 <macros>
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2 <token name="@VERSION@">1.0</token>
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4 <xml name="python_requirements">
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5 <requirements>
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6 <requirement type="package" version="3.6">python</requirement>
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7 <requirement type="package" version="0.20.2">scikit-learn</requirement>
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8 <requirement type="package" version="0.23.4">pandas</requirement>
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9 <requirement type="package" version="0.80">xgboost</requirement>
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10 <requirement type="package" version="0.9.13">asteval</requirement>
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11 <yield />
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12 </requirements>
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13 </xml>
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15 <xml name="macro_stdio">
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16 <stdio>
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17 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
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18 </stdio>
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19 </xml>
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22 <!--Generic interface-->
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24 <xml name="sl_Conditional" token_train="tabular" token_data="tabular" token_model="txt">
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25 <conditional name="selected_tasks">
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26 <param name="selected_task" type="select" label="Select a Classification Task">
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27 <option value="train" selected="true">Train a model</option>
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28 <option value="load">Load a model and predict</option>
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29 </param>
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30 <when value="load">
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31 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/>
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32 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
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33 <param name="header" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
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34 <conditional name="prediction_options">
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35 <param name="prediction_option" type="select" label="Select the type of prediction">
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36 <option value="predict">Predict class labels</option>
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37 <option value="advanced">Include advanced options</option>
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38 </param>
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39 <when value="predict">
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40 </when>
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41 <when value="advanced">
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42 </when>
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43 </conditional>
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44 </when>
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45 <when value="train">
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46 <conditional name="selected_algorithms">
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47 <yield />
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48 </conditional>
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49 </when>
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50 </conditional>
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51 </xml>
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52
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53 <xml name="advanced_section">
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54 <section name="options" title="Advanced Options" expanded="False">
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55 <yield />
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56 </section>
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57 </xml>
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58
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59
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60 <!--Generalized Linear Models-->
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61 <xml name="loss" token_help=" " token_select="false">
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62 <param argument="loss" type="select" label="Loss function" help="@HELP@">
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63 <option value="squared_loss" selected="@SELECT@">squared loss</option>
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64 <option value="huber">huber</option>
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65 <option value="epsilon_insensitive">epsilon insensitive</option>
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66 <option value="squared_epsilon_insensitive">squared epsilon insensitive</option>
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67 <yield/>
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68 </param>
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69 </xml>
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70
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71 <xml name="penalty" token_help=" ">
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72 <param argument="penalty" type="select" label="Penalty (regularization term)" help="@HELP@">
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73 <option value="l2" selected="true">l2</option>
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74 <option value="l1">l1</option>
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75 <option value="elasticnet">elastic net</option>
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76 <option value="none">none</option>
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77 <yield/>
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78 </param>
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79 </xml>
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80
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81 <xml name="l1_ratio" token_default_value="0.15" token_help=" ">
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82 <param argument="l1_ratio" type="float" value="@DEFAULT_VALUE@" label="Elastic Net mixing parameter" help="@HELP@"/>
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83 </xml>
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84
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85 <xml name="epsilon" token_default_value="0.1" token_help="Used if loss is ‘huber’, ‘epsilon_insensitive’, or ‘squared_epsilon_insensitive’. ">
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86 <param argument="epsilon" type="float" value="@DEFAULT_VALUE@" label="Epsilon (epsilon-sensitive loss functions only)" help="@HELP@"/>
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87 </xml>
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88
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89 <xml name="learning_rate_s" token_help=" " token_selected1="false" token_selected2="false">
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90 <param argument="learning_rate" type="select" optional="true" label="Learning rate schedule" help="@HELP@">
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91 <option value="optimal" selected="@SELECTED1@">optimal</option>
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92 <option value="constant">constant</option>
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93 <option value="invscaling" selected="@SELECTED2@">inverse scaling</option>
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94 <yield/>
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95 </param>
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96 </xml>
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97
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98 <xml name="eta0" token_default_value="0.0" token_help="Used with ‘constant’ or ‘invscaling’ schedules. ">
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99 <param argument="eta0" type="float" value="@DEFAULT_VALUE@" label="Initial learning rate" help="@HELP@"/>
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100 </xml>
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101
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102 <xml name="power_t" token_default_value="0.5" token_help=" ">
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103 <param argument="power_t" type="float" value="@DEFAULT_VALUE@" label="Exponent for inverse scaling learning rate" help="@HELP@"/>
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104 </xml>
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105
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106 <xml name="normalize" token_checked="false" token_help=" ">
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107 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Normalize samples before training" help=" "/>
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108 </xml>
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109
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110 <xml name="copy_X" token_checked="true" token_help=" ">
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111 <param argument="copy_X" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Use a copy of samples" help="If false, samples would be overwritten. "/>
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112 </xml>
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113
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114 <xml name="ridge_params">
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115 <expand macro="normalize"/>
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116 <expand macro="alpha" default_value="1.0"/>
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117 <expand macro="fit_intercept"/>
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118 <expand macro="max_iter" default_value=""/>
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119 <expand macro="tol" default_value="0.001" help_text="Precision of the solution. "/>
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120 <!--class_weight-->
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121 <expand macro="copy_X"/>
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122 <param argument="solver" type="select" value="" label="Solver to use in the computational routines" help=" ">
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123 <option value="auto" selected="true">auto</option>
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124 <option value="svd">svd</option>
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125 <option value="cholesky">cholesky</option>
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126 <option value="lsqr">lsqr</option>
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127 <option value="sparse_cg">sparse_cg</option>
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128 <option value="sag">sag</option>
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129 </param>
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130 <expand macro="random_state"/>
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131 </xml>
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132
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133 <!--Ensemble methods-->
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134 <xml name="n_estimators" token_default_value="10" token_help=" ">
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135 <param argument="n_estimators" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of trees in the forest" help="@HELP@"/>
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136 </xml>
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137
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138 <xml name="max_depth" token_default_value="" token_help=" ">
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139 <param argument="max_depth" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@"/>
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140 </xml>
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141
5
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142 <xml name="min_samples_split" token_type="integer" token_default_value="2" token_help=" ">
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143 <param argument="min_samples_split" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="Minimum number of samples required to split an internal node" help="@HELP@"/>
0
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144 </xml>
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145
5
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146 <xml name="min_samples_leaf" token_type="integer" token_default_value="1" token_label="Minimum number of samples in newly created leaves" token_help=" ">
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147 <param argument="min_samples_leaf" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP@"/>
0
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148 </xml>
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149
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150 <xml name="min_weight_fraction_leaf" token_default_value="0.0" token_help=" ">
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151 <param argument="min_weight_fraction_leaf" type="float" optional="true" value="@DEFAULT_VALUE@" label="Minimum weighted fraction of the input samples required to be at a leaf node" help="@HELP@"/>
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152 </xml>
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153
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154 <xml name="max_leaf_nodes" token_default_value="" token_help=" ">
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155 <param argument="max_leaf_nodes" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum number of leaf nodes in best-first method" help="@HELP@"/>
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156 </xml>
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157
5
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158 <xml name="min_impurity_decrease" token_default_value="0" token_help=" ">
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159 <param argument="min_impurity_decrease" type="float" value="@DEFAULT_VALUE@" optional="true" label="The threshold value of impurity for stopping node splitting" help="@HELP@"/>
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160 </xml>
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161
0
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162 <xml name="bootstrap" token_checked="true" token_help=" ">
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163 <param argument="bootstrap" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Use bootstrap samples for building trees." help="@HELP@"/>
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164 </xml>
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165
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166 <xml name="criterion" token_help=" ">
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167 <param argument="criterion" type="select" label="Function to measure the quality of a split" help=" ">
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168 <option value="gini" selected="true">Gini impurity</option>
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169 <option value="entropy">Information gain</option>
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170 <yield/>
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171 </param>
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172 </xml>
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173
5
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174 <xml name="criterion2" token_help="">
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175 <param argument="criterion" type="select" label="Function to measure the quality of a split" >
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176 <option value="mse">mse - mean squared error</option>
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177 <option value="mae">mae - mean absolute error</option>
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178 <yield/>
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179 </param>
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180 </xml>
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181
0
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182 <xml name="oob_score" token_checked="false" token_help=" ">
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183 <param argument="oob_score" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Use out-of-bag samples to estimate the generalization error" help="@HELP@"/>
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184 </xml>
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185
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186 <xml name="max_features">
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187 <conditional name="select_max_features">
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188 <param argument="max_features" type="select" label="max_features">
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189 <option value="auto" selected="true">auto - max_features=n_features</option>
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190 <option value="sqrt">sqrt - max_features=sqrt(n_features)</option>
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191 <option value="log2">log2 - max_features=log2(n_features)</option>
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192 <option value="number_input">I want to type the number in or input None type</option>
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193 </param>
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194 <when value="auto">
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195 </when>
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196 <when value="sqrt">
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197 </when>
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198 <when value="log2">
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199 </when>
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200 <when value="number_input">
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201 <param name="num_max_features" type="float" value="" optional="true" label="Input max_features number:" help="If int, consider the number of features at each split; If float, then max_features is a percentage and int(max_features * n_features) features are considered at each split."/>
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202 </when>
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203 </conditional>
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204 </xml>
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205
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206 <xml name="verbose" token_default_value="0" token_help="If 1 then it prints progress and performance once in a while. If greater than 1 then it prints progress and performance for every tree.">
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207 <param argument="verbose" type="integer" value="@DEFAULT_VALUE@" optional="true" label="Enable verbose output" help="@HELP@"/>
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208 </xml>
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209
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210 <xml name="learning_rate" token_default_value="1.0" token_help=" ">
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211 <param argument="learning_rate" type="float" optional="true" value="@DEFAULT_VALUE@" label="Learning rate" help="@HELP@"/>
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212 </xml>
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213
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214 <xml name="subsample" token_help=" ">
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215 <param argument="subsample" type="float" value="1.0" optional="true" label="The fraction of samples to be used for fitting the individual base learners" help="@HELP@"/>
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216 </xml>
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217
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218 <xml name="presort">
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219 <param argument="presort" type="select" label="Whether to presort the data to speed up the finding of best splits in fitting" >
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220 <option value="auto" selected="true">auto</option>
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221 <option value="true">true</option>
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222 <option value="false">false</option>
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223 </param>
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224 </xml>
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225
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226 <!--Parameters-->
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227 <xml name="tol" token_default_value="0.0" token_help_text="Early stopping heuristics based on the relative center changes. Set to default (0.0) to disable this convergence detection.">
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228 <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@"/>
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229 </xml>
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230
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231 <xml name="n_clusters" token_default_value="8">
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232 <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" "/>
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233 </xml>
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234
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235 <xml name="fit_intercept" token_checked="true">
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236 <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Estimate the intercept" help="If false, the data is assumed to be already centered."/>
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237 </xml>
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238
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239 <xml name="n_iter" token_default_value="5" token_help_text="The number of passes over the training data (aka epochs). ">
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240 <param argument="n_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@"/>
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241 </xml>
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242
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243 <xml name="shuffle" token_checked="true" token_help_text=" " token_label="Shuffle data after each iteration">
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244 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="@LABEL@" help="@HELP_TEXT@"/>
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245 </xml>
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246
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247 <xml name="random_state" token_default_value="" token_help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data. A fixed seed allows reproducible results. default=None.">
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248 <param argument="random_state" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Random seed number" help="@HELP_TEXT@"/>
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249 </xml>
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250
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251 <xml name="warm_start" token_checked="true" token_help_text="When set to True, reuse the solution of the previous call to fit as initialization,otherwise, just erase the previous solution.">
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252 <param argument="warm_start" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Perform warm start" help="@HELP_TEXT@"/>
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253 </xml>
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254
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255 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term.">
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256 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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257 </xml>
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258
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259 <!--xml name="class_weight" token_default_value="" token_help_text="">
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260 <param argument="class_weight" type="" optional="true" value="@DEFAULT_VALUE@" label="" help="@HELP_TEXT@"/>
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261 </xml-->
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262
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263 <xml name="alpha" token_default_value="0.0001" token_help_text="Constant that multiplies the regularization term if regularization is used. ">
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264 <param argument="alpha" type="float" optional="true" value="@DEFAULT_VALUE@" label="Regularization coefficient" help="@HELP_TEXT@"/>
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265 </xml>
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266
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267 <xml name="n_samples" token_default_value="100" token_help_text="The total number of points equally divided among clusters.">
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268 <param argument="n_samples" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of samples" help="@HELP_TEXT@"/>
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269 </xml>
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270
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271 <xml name="n_features" token_default_value="2" token_help_text="Number of different numerical properties produced for each sample.">
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272 <param argument="n_features" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of features" help="@HELP_TEXT@"/>
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273 </xml>
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274
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275 <xml name="noise" token_default_value="0.0" token_help_text="Floating point number. ">
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276 <param argument="noise" type="float" optional="true" value="@DEFAULT_VALUE@" label="Standard deviation of the Gaussian noise added to the data" help="@HELP_TEXT@"/>
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277 </xml>
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278
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279 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term. ">
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280 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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281 </xml>
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282
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283 <xml name="max_iter" token_default_value="300" token_label="Maximum number of iterations per single run" token_help_text=" ">
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284 <param argument="max_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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285 </xml>
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286
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287 <xml name="n_init" token_default_value="10" >
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288 <param argument="n_init" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of runs with different centroid seeds" help=" "/>
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289 </xml>
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290
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291 <xml name="init">
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292 <param argument="init" type="select" label="Centroid initialization method" help="''k-means++'' selects initial cluster centers that speed up convergence. ''random'' chooses k observations (rows) at random from data as initial centroids.">
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293 <option value="k-means++">k-means++</option>
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294 <option value="random">random</option>
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295 </param>
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296 </xml>
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297
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298 <xml name="gamma" token_default_value="1.0" token_label="Scaling parameter" token_help_text=" ">
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299 <param argument="gamma" type="float" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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300 </xml>
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301
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302 <xml name="degree" token_default_value="3" token_label="Degree of the polynomial" token_help_text=" ">
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303 <param argument="degree" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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304 </xml>
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305
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306 <xml name="coef0" token_default_value="1" token_label="Zero coefficient" token_help_text=" ">
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307 <param argument="coef0" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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308 </xml>
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309
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310 <xml name="pos_label" token_default_value="">
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311 <param argument="pos_label" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Label of the positive class" help=" "/>
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312 </xml>
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313
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314 <xml name="average">
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315 <param argument="average" type="select" optional="true" label="Averaging type" help=" ">
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316 <option value="micro">Calculate metrics globally by counting the total true positives, false negatives and false positives. (micro)</option>
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317 <option value="samples">Calculate metrics for each instance, and find their average. Only meaningful for multilabel. (samples)</option>
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318 <option value="macro">Calculate metrics for each label, and find their unweighted mean. This does not take label imbalance into account. (macro)</option>
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319 <option value="weighted">Calculate metrics for each label, and find their average, weighted by support (the number of true instances for each label). This alters ‘macro’ to account for label imbalance; it can result in an F-score that is not between precision and recall. (weighted)</option>
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320 <option value="None">None</option>
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321 <yield/>
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322 </param>
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323 </xml>
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324
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325 <xml name="beta">
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326 <param argument="beta" type="float" value="1.0" label="The strength of recall versus precision in the F-score" help=" "/>
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327 </xml>
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328
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329
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330 <!--Data interface-->
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331
10
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332 <xml name="samples_tabular" token_multiple1="false" token_multiple2="false">
0
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333 <param name="infile1" type="data" format="tabular" label="Training samples dataset:"/>
10
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334 <param name="header1" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
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335 <conditional name="column_selector_options_1">
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336 <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@"/>
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337 </conditional>
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338 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels or target values:"/>
10
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339 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
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340 <conditional name="column_selector_options_2">
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341 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE2@" infile="infile2"/>
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342 </conditional>
0
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343 <yield/>
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344 </xml>
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345
10
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346 <xml name="samples_column_selector_options" token_column_option="selected_column_selector_option" token_col_name="col1" token_multiple="False" token_infile="infile1">
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347 <param name="@COLUMN_OPTION@" type="select" label="Choose how to select data by column:">
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348 <option value="by_index_number" selected="true">Select columns by column index number(s)</option>
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349 <option value="all_but_by_index_number">All columns BUT by column index number(s)</option>
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350 <option value="by_header_name">Select columns by column header name(s)</option>
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351 <option value="all_but_by_header_name">All columns BUT by column header name(s)</option>
10
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352 <option value="all_columns">All columns</option>
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353 </param>
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354 <when value="by_index_number">
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355 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" data_ref="@INFILE@" label="Select target column(s):"/>
93d391c5ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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parents: 9
diff changeset
356 </when>
23
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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parents: 21
diff changeset
357 <when value="all_but_by_index_number">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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parents: 21
diff changeset
358 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" data_ref="@INFILE@" label="Select target column(s):"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
359 </when>
12
cb14b6827f70 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents: 11
diff changeset
360 <when value="by_header_name">
15
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parents: 13
diff changeset
361 <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="Comma-separated string. For example: target1,target2"/>
12
cb14b6827f70 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents: 11
diff changeset
362 </when>
cb14b6827f70 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents: 11
diff changeset
363 <when value="all_but_by_header_name">
15
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
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parents: 13
diff changeset
364 <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="Comma-separated string. For example: target1,target2"/>
12
cb14b6827f70 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
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parents: 11
diff changeset
365 </when>
10
93d391c5ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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parents: 9
diff changeset
366 <when value="all_columns">
93d391c5ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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parents: 9
diff changeset
367 </when>
93d391c5ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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parents: 9
diff changeset
368 </xml>
93d391c5ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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parents: 9
diff changeset
369
0
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
370 <xml name="clf_inputs_extended" token_label1=" " token_label2=" " token_multiple="False">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
371 <conditional name="true_columns">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
372 <param name="selected_input1" type="select" label="Select the input type of true labels dataset:">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
373 <option value="tabular" selected="true">Tabular</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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374 <option value="sparse">Sparse</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
375 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
376 <when value="tabular">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
377 <param name="infile1" type="data" label="@LABEL1@"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
378 <param name="col1" type="data_column" data_ref="infile1" label="Select the target column:"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
379 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
380 <when value="sparse">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
381 <param name="infile1" type="data" format="txt" label="@LABEL1@"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
382 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
383 </conditional>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
384 <conditional name="predicted_columns">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
385 <param name="selected_input2" type="select" label="Select the input type of predicted labels dataset:">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
386 <option value="tabular" selected="true">Tabular</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
387 <option value="sparse">Sparse</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
388 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
389 <when value="tabular">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
390 <param name="infile2" type="data" label="@LABEL2@"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
391 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
392 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
393 <when value="sparse">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
394 <param name="infile2" type="data" format="txt" label="@LABEL1@"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
395 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
396 </conditional>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
397 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
398
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
399 <xml name="clf_inputs" token_label1="Dataset containing true labels (tabular):" token_label2="Dataset containing predicted values (tabular):" token_multiple1="False" token_multiple="False">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
400 <param name="infile1" type="data" format="tabular" label="@LABEL1@"/>
7
cdb7948427aa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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parents: 6
diff changeset
401 <param name="header1" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
10
93d391c5ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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parents: 9
diff changeset
402 <conditional name="column_selector_options_1">
93d391c5ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
bgruening
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diff changeset
403 <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@"/>
93d391c5ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
bgruening
parents: 9
diff changeset
404 </conditional>
0
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
405 <param name="infile2" type="data" format="tabular" label="@LABEL2@"/>
7
cdb7948427aa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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parents: 6
diff changeset
406 <param name="header2" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
10
93d391c5ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
bgruening
parents: 9
diff changeset
407 <conditional name="column_selector_options_2">
93d391c5ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
bgruening
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diff changeset
408 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE@" infile="infile2"/>
93d391c5ba50 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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parents: 9
diff changeset
409 </conditional>
0
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
410 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
411
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
412 <xml name="multiple_input" token_name="input_files" token_max_num="10" token_format="txt" token_label="Sparse matrix file (.mtx, .txt)" token_help_text="Specify a sparse matrix file in .txt format.">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
413 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
414 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
415 </repeat>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
416 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
417
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
418 <xml name="sparse_target" token_label1="Select a sparse matrix:" token_label2="Select the tabular containing true labels:" token_multiple="False" token_format1="txt" token_format2="tabular" token_help1="" token_help2="">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
419 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
420 <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
421 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
422 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
423
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
424 <xml name="sl_mixed_input">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
425 <conditional name="input_options">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
426 <param name="selected_input" type="select" label="Select input type:">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
427 <option value="tabular" selected="true">tabular data</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
428 <option value="sparse">sparse matrix</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
429 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
430 <when value="tabular">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
431 <expand macro="samples_tabular" multiple1="true"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
432 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
433 <when value="sparse">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
434 <expand macro="sparse_target"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
435 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
436 </conditional>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
437 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
438
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
439 <!--Advanced options-->
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
440 <xml name="nn_advanced_options">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
441 <section name="options" title="Advanced Options" expanded="False">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
442 <yield/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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443 <param argument="weights" type="select" label="Weight function" help="Used in prediction.">
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444 <option value="uniform" selected="true">Uniform weights. All points in each neighborhood are weighted equally. (Uniform)</option>
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445 <option value="distance">Weight points by the inverse of their distance. (Distance)</option>
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446 </param>
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447 <param argument="algorithm" type="select" label="Neighbor selection algorithm" help=" ">
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448 <option value="auto" selected="true">Auto</option>
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449 <option value="ball_tree">BallTree</option>
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450 <option value="kd_tree">KDTree</option>
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451 <option value="brute">Brute-force</option>
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452 </param>
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453 <param argument="leaf_size" type="integer" value="30" label="Leaf size" help="Used with BallTree and KDTree. Affects the time and memory usage of the constructed tree."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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454 <!--param name="metric"-->
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455 <!--param name="p"-->
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456 <!--param name="metric_params"-->
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457 </section>
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458 </xml>
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459
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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460 <xml name="svc_advanced_options">
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461 <section name="options" title="Advanced Options" expanded="False">
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462 <yield/>
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463 <param argument="kernel" type="select" optional="true" label="Kernel type" help="Kernel type to be used in the algorithm. If none is given, ‘rbf’ will be used.">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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464 <option value="rbf" selected="true">rbf</option>
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465 <option value="linear">linear</option>
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466 <option value="poly">poly</option>
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467 <option value="sigmoid">sigmoid</option>
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468 <option value="precomputed">precomputed</option>
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469 </param>
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470 <param argument="degree" type="integer" optional="true" value="3" label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/>
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471 <!--TODO: param argument="gamma" float, optional (default=’auto’) -->
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472 <param argument="coef0" type="float" optional="true" value="0.0" label="Zero coefficient (polynomial and sigmoid kernels only)"
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473 help="Independent term in kernel function. dafault: 0.0 "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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474 <param argument="shrinking" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
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475 label="Use the shrinking heuristic" help=" "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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476 <param argument="probability" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false"
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477 label="Enable probability estimates. " help="This must be enabled prior to calling fit, and will slow down that method."/>
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478 <!-- param argument="cache_size"-->
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479 <!--expand macro="class_weight"/-->
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480 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. "/>
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481 <expand macro="max_iter" default_value="-1" label="Solver maximum number of iterations" help_text="Hard limit on iterations within solver, or -1 for no limit."/>
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482 <!--param argument="decision_function_shape"-->
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483 <expand macro="random_state" help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data for probability estimation. A fixed seed allows reproducible results."/>
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484 </section>
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485 </xml>
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486
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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487 <xml name="spectral_clustering_advanced_options">
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488 <section name="options" title="Advanced Options" expanded="False">
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489 <expand macro="n_clusters"/>
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490 <param argument="eigen_solver" type="select" value="" label="Eigen solver" help="The eigenvalue decomposition strategy to use.">
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491 <option value="arpack" selected="true">arpack</option>
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492 <option value="lobpcg">lobpcg</option>
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493 <option value="amg">amg</option>
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494 <!--None-->
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495 </param>
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496 <expand macro="random_state"/>
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497 <expand macro="n_init"/>
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498 <param argument="gamma" type="float" optional="true" value="1.0" label="Kernel scaling factor" help="Scaling factor of RBF, polynomial, exponential chi^2 and sigmoid affinity kernel. Ignored for affinity=''nearest_neighbors''."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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499 <param argument="affinity" type="select" label="Affinity" help="Affinity kernel to use. ">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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500 <option value="rbf" selected="true">RBF</option>
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501 <option value="precomputed">precomputed</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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502 <option value="nearest_neighbors">Nearset neighbors</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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503 </param>
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504 <param argument="n_neighbors" type="integer" optional="true" value="10" label="Number of neighbors" help="Number of neighbors to use when constructing the affinity matrix using the nearest neighbors method. Ignored for affinity=''rbf''"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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505 <!--param argument="eigen_tol"-->
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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506 <param argument="assign_labels" type="select" label="Assign labels" help="The strategy to use to assign labels in the embedding space.">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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507 <option value="kmeans" selected="true">kmeans</option>
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508 <option value="discretize">discretize</option>
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509 </param>
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510 <param argument="degree" type="integer" optional="true" value="3"
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511 label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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512 <param argument="coef0" type="integer" optional="true" value="1"
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513 label="Zero coefficient (polynomial and sigmoid kernels only)" help="Ignored by other kernels. dafault : 1 "/>
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514 <!--param argument="kernel_params"-->
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515 </section>
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516 </xml>
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517
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518 <xml name="minibatch_kmeans_advanced_options">
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519 <section name="options" title="Advanced Options" expanded="False">
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520 <expand macro="n_clusters"/>
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521 <expand macro="init"/>
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522 <expand macro="n_init" default_value="3"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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523 <expand macro="max_iter" default_value="100"/>
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524 <expand macro="tol" help_text="Early stopping heuristics based on normalized center change. To disable set to 0.0 ."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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525 <expand macro="random_state"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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526 <param argument="batch_size" type="integer" optional="true" value="100" label="Batch size" help="Size of the mini batches."/>
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527 <!--param argument="compute_labels"-->
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528 <param argument="max_no_improvement" type="integer" optional="true" value="10" label="Maximum number of improvement attempts" help="
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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529 Convergence detection based on inertia (the consecutive number of mini batches that doe not yield an improvement on the smoothed inertia).
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diff changeset
530 To disable, set max_no_improvement to None. "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
531 <param argument="init_size" type="integer" optional="true" value="" label="Number of random initialization samples" help="Number of samples to randomly sample for speeding up the initialization . ( default: 3 * batch_size )"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
532 <param argument="reassignment_ratio" type="float" optional="true" value="0.01" label="Re-assignment ratio" help="Controls the fraction of the maximum number of counts for a center to be reassigned. Higher values yield better clustering results."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
533 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
534 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
535
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
536 <xml name="kmeans_advanced_options">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
537 <section name="options" title="Advanced Options" expanded="False">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
538 <expand macro="n_clusters"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
539 <expand macro="init"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
540 <expand macro="n_init"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
541 <expand macro="max_iter"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
542 <expand macro="tol" default_value="0.0001" help_text="Relative tolerance with regards to inertia to declare convergence."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
543 <!--param argument="precompute_distances"/-->
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
544 <expand macro="random_state"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
545 <param argument="copy_x" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Use a copy of data for precomputing distances" help="Mofifying the original data introduces small numerical differences caused by subtracting and then adding the data mean."/>
23
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
546 <expand macro="kmeans_algorithm"/>
0
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
547 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
548 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
549
23
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
550 <xml name="kmeans_algorithm">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
551 <param argument="algorithm" type="select" label="K-means algorithm to use:">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
552 <option value="auto" selected="true">auto</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
553 <option value="full">full</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
554 <option value="elkan">elkan</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
555 </param>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
556 </xml>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
557
0
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
558 <xml name="birch_advanced_options">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
559 <section name="options" title="Advanced Options" expanded="False">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
560 <param argument="threshold" type="float" optional="true" value="0.5" label="Subcluster radius threshold" help="The radius of the subcluster obtained by merging a new sample; the closest subcluster should be less than the threshold to avoid a new subcluster."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
561 <param argument="branching_factor" type="integer" optional="true" value="50" label="Maximum number of subclusters per branch" help="Maximum number of CF subclusters in each node."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
562 <expand macro="n_clusters" default_value="3"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
563 <!--param argument="compute_labels"/-->
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
564 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
565 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
566
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
567 <xml name="dbscan_advanced_options">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
568 <section name="options" title="Advanced Options" expanded="False">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
569 <param argument="eps" type="float" optional="true" value="0.5" label="Maximum neighborhood distance" help="The maximum distance between two samples for them to be considered as in the same neighborhood."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
570 <param argument="min_samples" type="integer" optional="true" value="5" label="Minimal core point density" help="The number of samples (or total weight) in a neighborhood for a point (including the point itself) to be considered as a core point."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
571 <param argument="metric" type="text" optional="true" value="euclidean" label="Metric" help="The metric to use when calculating distance between instances in a feature array."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
572 <param argument="algorithm" type="select" label="Pointwise distance computation algorithm" help="The algorithm to be used by the NearestNeighbors module to compute pointwise distances and find nearest neighbors.">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
573 <option value="auto" selected="true">auto</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
574 <option value="ball_tree">ball_tree</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
575 <option value="kd_tree">kd_tree</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
576 <option value="brute">brute</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
577 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
578 <param argument="leaf_size" type="integer" optional="true" value="30" label="Leaf size" help="Leaf size passed to BallTree or cKDTree. Memory and time efficieny factor in tree constrution and querying."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
579 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
580 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
581
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
582 <xml name="clustering_algorithms_options">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
583 <conditional name="algorithm_options">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
584 <param name="selected_algorithm" type="select" label="Clustering Algorithm">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
585 <option value="KMeans" selected="true">KMeans</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
586 <option value="SpectralClustering">Spectral Clustering</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
587 <option value="MiniBatchKMeans">Mini Batch KMeans</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
588 <option value="DBSCAN">DBSCAN</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
589 <option value="Birch">Birch</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
590 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
591 <when value="KMeans">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
592 <expand macro="kmeans_advanced_options"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
593 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
594 <when value="DBSCAN">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
595 <expand macro="dbscan_advanced_options"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
596 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
597 <when value="Birch">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
598 <expand macro="birch_advanced_options"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
599 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
600 <when value="SpectralClustering">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
601 <expand macro="spectral_clustering_advanced_options"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
602 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
603 <when value="MiniBatchKMeans">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
604 <expand macro="minibatch_kmeans_advanced_options"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
605 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
606 </conditional>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
607 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
608
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
609 <xml name="distance_metrics">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
610 <param argument="metric" type="select" label="Distance metric" help=" ">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
611 <option value="euclidean" selected="true">euclidean</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
612 <option value="cityblock">cityblock</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
613 <option value="cosine">cosine</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
614 <option value="l1">l1</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
615 <option value="l2">l2</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
616 <option value="manhattan">manhattan</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
617 <yield/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
618 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
619 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
620
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
621 <xml name="distance_nonsparse_metrics">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
622 <option value="braycurtis">braycurtis</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
623 <option value="canberra">canberra</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
624 <option value="chebyshev">chebyshev</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
625 <option value="correlation">correlation</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
626 <option value="dice">dice</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
627 <option value="hamming">hamming</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
628 <option value="jaccard">jaccard</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
629 <option value="kulsinski">kulsinski</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
630 <option value="mahalanobis">mahalanobis</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
631 <option value="matching">matching</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
632 <option value="minkowski">minkowski</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
633 <option value="rogerstanimoto">rogerstanimoto</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
634 <option value="russellrao">russellrao</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
635 <option value="seuclidean">seuclidean</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
636 <option value="sokalmichener">sokalmichener</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
637 <option value="sokalsneath">sokalsneath</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
638 <option value="sqeuclidean">sqeuclidean</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
639 <option value="yule">yule</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
640 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
641
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
642 <xml name="pairwise_kernel_metrics">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
643 <param argument="metric" type="select" label="Pirwise Kernel metric" help=" ">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
644 <option value="rbf" selected="true">rbf</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
645 <option value="sigmoid">sigmoid</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
646 <option value="polynomial">polynomial</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
647 <option value="linear" selected="true">linear</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
648 <option value="chi2">chi2</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
649 <option value="additive_chi2">additive_chi2</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
650 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
651 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
652
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
653 <xml name="sparse_pairwise_metric_functions">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
654 <param name="selected_metric_function" type="select" label="Select the pairwise metric you want to compute:">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
655 <option value="euclidean_distances" selected="true">Euclidean distance matrix</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
656 <option value="pairwise_distances">Distance matrix</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
657 <option value="pairwise_distances_argmin">Minimum distances between one point and a set of points</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
658 <yield/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
659 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
660 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
661
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
662 <xml name="pairwise_metric_functions">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
663 <option value="additive_chi2_kernel" >Additive chi-squared kernel</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
664 <option value="chi2_kernel">Exponential chi-squared kernel</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
665 <option value="linear_kernel">Linear kernel</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
666 <option value="manhattan_distances">L1 distances</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
667 <option value="pairwise_kernels">Kernel</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
668 <option value="polynomial_kernel">Polynomial kernel</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
669 <option value="rbf_kernel">Gaussian (rbf) kernel</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
670 <option value="laplacian_kernel">Laplacian kernel</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
671 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
672
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
673 <xml name="sparse_pairwise_condition">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
674 <when value="pairwise_distances">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
675 <section name="options" title="Advanced Options" expanded="False">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
676 <expand macro="distance_metrics">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
677 <yield/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
678 </expand>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
679 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
680 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
681 <when value="euclidean_distances">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
682 <section name="options" title="Advanced Options" expanded="False">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
683 <param argument="squared" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false"
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
684 label="Return squared Euclidean distances" help=" "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
685 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
686 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
687 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
688
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
689 <xml name="argmin_distance_condition">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
690 <when value="pairwise_distances_argmin">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
691 <section name="options" title="Advanced Options" expanded="False">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
692 <param argument="axis" type="integer" optional="true" value="1" label="Axis" help="Axis along which the argmin and distances are to be computed."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
693 <expand macro="distance_metrics">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
694 <yield/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
695 </expand>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
696 <param argument="batch_size" type="integer" optional="true" value="500" label="Batch size" help="Number of rows to be processed in each batch run."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
697 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
698 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
699 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
700
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
701 <xml name="sparse_preprocessors">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
702 <param name="selected_pre_processor" type="select" label="Select a preprocessor:">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
703 <option value="StandardScaler" selected="true">Standard Scaler (Standardizes features by removing the mean and scaling to unit variance)</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
704 <option value="Binarizer">Binarizer (Binarizes data)</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
705 <option value="Imputer">Imputer (Completes missing values)</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
706 <option value="MaxAbsScaler">Max Abs Scaler (Scales features by their maximum absolute value)</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
707 <option value="Normalizer">Normalizer (Normalizes samples individually to unit norm)</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
708 <yield/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
709 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
710 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
711
15
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
712 <xml name="sparse_preprocessors_ext">
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
713 <expand macro="sparse_preprocessors">
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
714 <option value="KernelCenterer">Kernel Centerer (Centers a kernel matrix)</option>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
715 <option value="MinMaxScaler">Minmax Scaler (Scales features to a range)</option>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
716 <option value="PolynomialFeatures">Polynomial Features (Generates polynomial and interaction features)</option>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
717 <option value="RobustScaler">Robust Scaler (Scales features using outlier-invariance statistics)</option>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
718 </expand>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
719 </xml>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
720
0
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
721 <xml name="sparse_preprocessor_options">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
722 <when value="Binarizer">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
723 <section name="options" title="Advanced Options" expanded="False">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
724 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
725 label="Use a copy of data for precomputing binarization" help=" "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
726 <param argument="threshold" type="float" optional="true" value="0.0"
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
727 label="Threshold"
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
728 help="Feature values below or equal to this are replaced by 0, above it by 1. Threshold may not be less than 0 for operations on sparse matrices. "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
729 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
730 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
731 <when value="Imputer">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
732 <section name="options" title="Advanced Options" expanded="False">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
733 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
734 label="Use a copy of data for precomputing imputation" help=" "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
735 <param argument="strategy" type="select" optional="true" label="Imputation strategy" help=" ">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
736 <option value="mean" selected="true">Replace missing values using the mean along the axis</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
737 <option value="median">Replace missing values using the median along the axis</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
738 <option value="most_frequent">Replace missing using the most frequent value along the axis</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
739 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
740 <param argument="missing_values" type="text" optional="true" value="NaN"
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
741 label="Placeholder for missing values" help="For missing values encoded as numpy.nan, use the string value “NaN”"/>
23
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
742 <!--param argument="axis" type="boolean" optional="true" truevalue="1" falsevalue="0"
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
743 label="Impute along axis = 1" help="If fasle, axis = 0 is selected for imputation. "/> -->
0
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
744 <!--param argument="axis" type="select" optional="true" label="The axis along which to impute" help=" ">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
745 <option value="0" selected="true">Impute along columns</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
746 <option value="1">Impute along rows</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
747 </param-->
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
748 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
749 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
750 <when value="StandardScaler">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
751 <section name="options" title="Advanced Options" expanded="False">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
752 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
753 label="Use a copy of data for performing inplace scaling" help=" "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
754 <param argument="with_mean" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
755 label="Center the data before scaling" help=" "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
756 <param argument="with_std" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
757 label="Scale the data to unit variance (or unit standard deviation)" help=" "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
758 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
759 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
760 <when value="MaxAbsScaler">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
761 <section name="options" title="Advanced Options" expanded="False">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
762 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
763 label="Use a copy of data for precomputing scaling" help=" "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
764 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
765 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
766 <when value="Normalizer">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
767 <section name="options" title="Advanced Options" expanded="False">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
768 <param argument="norm" type="select" optional="true" label="The norm to use to normalize non zero samples" help=" ">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
769 <option value="l1" selected="true">l1</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
770 <option value="l2">l2</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
771 <option value="max">max</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
772 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
773 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
774 label="Use a copy of data for precomputing row normalization" help=" "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
775 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
776 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
777 <yield/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
778 </xml>
15
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
779
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
780 <xml name="sparse_preprocessor_options_ext">
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
781 <expand macro="sparse_preprocessor_options">
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
782 <when value="KernelCenterer">
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
783 <section name="options" title="Advanced Options" expanded="False">
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
784 </section>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
785 </when>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
786 <when value="MinMaxScaler">
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
787 <section name="options" title="Advanced Options" expanded="False">
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
788 <!--feature_range-->
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
789 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
790 label="Use a copy of data for precomputing normalization" help=" "/>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
791 </section>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
792 </when>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
793 <when value="PolynomialFeatures">
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
794 <section name="options" title="Advanced Options" expanded="False">
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
795 <param argument="degree" type="integer" optional="true" value="2" label="The degree of the polynomial features " help=""/>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
796 <param argument="interaction_only" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Produce interaction features only" help="(Features that are products of at most degree distinct input features) "/>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
797 <param argument="include_bias" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Include a bias column" help="Feature in which all polynomial powers are zero "/>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
798 </section>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
799 </when>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
800 <when value="RobustScaler">
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
801 <section name="options" title="Advanced Options" expanded="False">
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
802 <!--=True, =True, copy=True-->
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
803 <param argument="with_centering" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
804 label="Center the data before scaling" help=" "/>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
805 <param argument="with_scaling" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
806 label="Scale the data to interquartile range" help=" "/>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
807 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
808 label="Use a copy of data for inplace scaling" help=" "/>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
809 </section>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
810 </when>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
811 </expand>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
812 </xml>
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
813
23
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
814 <xml name="cv_splitter">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
815 <option value="default" selected="true">default splitter</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
816 <option value="KFold">KFold</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
817 <option value="StratifiedKFold">StratifiedKFold</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
818 <option value="LeaveOneOut">LeaveOneOut</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
819 <option value="LeavePOut">LeavePOut</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
820 <option value="RepeatedKFold">RepeatedKFold</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
821 <option value="RepeatedStratifiedKFold">RepeatedStratifiedKFold</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
822 <option value="ShuffleSplit">ShuffleSplit</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
823 <option value="StratifiedShuffleSplit">StratifiedShuffleSplit</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
824 <option value="TimeSeriesSplit">TimeSeriesSplit</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
825 <option value="PredefinedSplit">PredefinedSplit</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
826 <yield/>
16
0b57ef8831fb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 15
diff changeset
827 </xml>
0b57ef8831fb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 15
diff changeset
828
23
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
829 <xml name="cv_splitter_options">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
830 <when value="default">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
831 <expand macro="cv_n_splits"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
832 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
833 <when value="KFold">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
834 <expand macro="cv_n_splits"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
835 <expand macro="cv_shuffle"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
836 <expand macro="random_state"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
837 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
838 <when value="StratifiedKFold">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
839 <expand macro="cv_n_splits"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
840 <expand macro="cv_shuffle"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
841 <expand macro="random_state"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
842 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
843 <when value="LeaveOneOut">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
844 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
845 <when value="LeavePOut">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
846 <param argument="p" type="integer" value="" label="p" help="Integer. Size of the test sets."/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
847 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
848 <when value="RepeatedKFold">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
849 <expand macro="cv_n_splits" value="5"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
850 <param argument="n_repeats" type="integer" value="10" label="n_repeats" help="Number of times cross-validator needs to be repeated." />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
851 <expand macro="random_state" />
16
0b57ef8831fb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 15
diff changeset
852 </when>
23
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
853 <when value="RepeatedStratifiedKFold">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
854 <expand macro="cv_n_splits" value="5"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
855 <param argument="n_repeats" type="integer" value="10" label="n_repeats" help="Number of times cross-validator needs to be repeated." />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
856 <expand macro="random_state" />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
857 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
858 <when value="ShuffleSplit">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
859 <expand macro="cv_n_splits" value="10" help="Number of re-shuffling and splitting iterations."/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
860 <expand macro="cv_test_size" value="0.1" />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
861 <expand macro="random_state"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
862 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
863 <when value="StratifiedShuffleSplit">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
864 <expand macro="cv_n_splits" value="10" help="Number of re-shuffling and splitting iterations."/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
865 <expand macro="cv_test_size" value="0.1" />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
866 <expand macro="random_state"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
867 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
868 <when value="TimeSeriesSplit">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
869 <expand macro="cv_n_splits"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
870 <param argument="max_train_size" type="integer" value="" optional="true" label="Maximum size of the training set" help="Maximum size for a single training set." />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
871 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
872 <when value="PredefinedSplit">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
873 <param argument="test_fold" type="text" value="" area="true" label="test_fold" help="List, e.g., [0, 1, -1, 1], represents two test sets, [X[0]] and [X[1], X[3]], X[2] is excluded from any test set due to '-1'."/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
874 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
875 <yield/>
9
1b2b2d304e44 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 8
diff changeset
876 </xml>
15
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
877
19
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
878 <xml name="cv">
23
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
879 <conditional name="cv_selector">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
880 <param name="selected_cv" type="select" label="Select the cv splitter:">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
881 <expand macro="cv_splitter">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
882 <option value="GroupKFold">GroupKFold</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
883 <option value="GroupShuffleSplit">GroupShuffleSplit</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
884 <option value="LeaveOneGroupOut">LeaveOneGroupOut</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
885 <option value="LeavePGroupsOut">LeavePGroupsOut</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
886 </expand>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
887 </param>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
888 <expand macro="cv_splitter_options">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
889 <when value="GroupKFold">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
890 <expand macro="cv_n_splits"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
891 <expand macro="cv_groups" />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
892 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
893 <when value="GroupShuffleSplit">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
894 <expand macro="cv_n_splits" value="5"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
895 <expand macro="cv_test_size"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
896 <expand macro="random_state"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
897 <expand macro="cv_groups"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
898 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
899 <when value="LeaveOneGroupOut">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
900 <expand macro="cv_groups"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
901 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
902 <when value="LeavePGroupsOut">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
903 <param argument="n_groups" type="integer" value="" label="n_groups" help="Number of groups (p) to leave out in the test split." />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
904 <expand macro="cv_groups"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
905 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
906 </expand>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
907 </conditional>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
908 </xml>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
909
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
910 <xml name="cv_reduced">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
911 <conditional name="cv_selector">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
912 <param name="selected_cv" type="select" label="Select the cv splitter:">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
913 <expand macro="cv_splitter"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
914 </param>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
915 <expand macro="cv_splitter_options"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
916 </conditional>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
917 </xml>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
918
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
919 <xml name="cv_n_splits" token_value="3" token_help="Number of folds. Must be at least 2.">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
920 <param argument="n_splits" type="integer" value="@VALUE@" min="2" label="n_splits" help="@HELP@"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
921 </xml>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
922
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
923 <xml name="cv_shuffle">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
924 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Whether to shuffle data before splitting" />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
925 </xml>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
926
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
927 <xml name="cv_test_size" token_value="0.2">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
928 <param argument="test_size" type="float" value="@VALUE@" min="0.0" label="Portion or number of the test set" help="0.0-1.0, proportion of the dataset to include in the test split; >1, integer only, the absolute number of test samples "/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
929 </xml>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
930
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
931 <xml name="cv_groups" >
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
932 <param argument="groups" type="text" value="" area="true" label="Groups" help="Group lables in a list. e.g., [1, 1, 2, 2, 3, 3, 3]"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
933 </xml>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
934
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
935 <xml name="feature_selection_algorithms">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
936 <option value="SelectKBest" selected="true">SelectKBest - Select features according to the k highest scores</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
937 <option value="GenericUnivariateSelect">GenericUnivariateSelect - Univariate feature selector with configurable strategy</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
938 <option value="SelectPercentile">SelectPercentile - Select features according to a percentile of the highest scores</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
939 <option value="SelectFpr">SelectFpr - Filter: Select the p-values below alpha based on a FPR test</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
940 <option value="SelectFdr">SelectFdr - Filter: Select the p-values for an estimated false discovery rate</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
941 <option value="SelectFwe">SelectFwe - Filter: Select the p-values corresponding to Family-wise error rate</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
942 <option value="VarianceThreshold">VarianceThreshold - Feature selector that removes all low-variance features</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
943 <option value="SelectFromModel">SelectFromModel - Meta-transformer for selecting features based on importance weights</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
944 <option value="RFE">RFE - Feature ranking with recursive feature elimination</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
945 <option value="RFECV">RFECV - Feature ranking with recursive feature elimination and cross-validated selection of the best number of features</option>
19
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
946 </xml>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
947
23
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
948 <xml name="feature_selection_algorithm_details">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
949 <when value="GenericUnivariateSelect">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
950 <expand macro="feature_selection_score_function" />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
951 <section name="options" title="Advanced Options" expanded="False">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
952 <param argument="mode" type="select" label="Feature selection mode">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
953 <option value="percentile">percentile</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
954 <option value="k_best">k_best</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
955 <option value="fpr">fpr</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
956 <option value="fdr">fdr</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
957 <option value="fwe">fwe</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
958 </param>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
959 <param argument="param" type="float" value="" optional="true" label="Parameter of the corresponding mode" help="float or int depending on the feature selection mode" />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
960 </section>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
961 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
962 <when value="SelectPercentile">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
963 <expand macro="feature_selection_score_function" />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
964 <section name="options" title="Advanced Options" expanded="False">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
965 <param argument="percentile" type="integer" value="10" optional="True" label="Percent of features to keep" />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
966 </section>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
967 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
968 <when value="SelectKBest">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
969 <expand macro="feature_selection_score_function" />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
970 <section name="options" title="Advanced Options" expanded="False">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
971 <param argument="k" type="integer" value="10" optional="True" label="Number of top features to select" help="No 'all' option is supported." />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
972 </section>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
973 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
974 <when value="SelectFpr">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
975 <expand macro="feature_selection_score_function" />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
976 <section name="options" title="Advanced Options" expanded="False">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
977 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest p-value for features to be kept."/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
978 </section>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
979 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
980 <when value="SelectFdr">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
981 <expand macro="feature_selection_score_function" />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
982 <section name="options" title="Advanced Options" expanded="False">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
983 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep."/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
984 </section>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
985 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
986 <when value="SelectFwe">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
987 <expand macro="feature_selection_score_function" />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
988 <section name="options" title="Advanced Options" expanded="False">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
989 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep."/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
990 </section>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
991 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
992 <when value="VarianceThreshold">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
993 <section name="options" title="Options" expanded="False">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
994 <param argument="threshold" type="float" value="" optional="True" label="Threshold" help="Features with a training-set variance lower than this threshold will be removed."/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
995 </section>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
996 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
997 </xml>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
998
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
999 <xml name="feature_selection_SelectFromModel">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1000 <when value="SelectFromModel">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1001 <conditional name="model_inputter">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1002 <param name="input_mode" type="select" label="Construct a new estimator from a selection list?" >
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1003 <option value="new" selected="true">Yes</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1004 <option value="prefitted">No. Load a prefitted estimator</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1005 </param>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1006 <when value="new">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1007 <expand macro="estimator_selector_fs"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1008 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1009 <when value="prefitted">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1010 <param name="fitted_estimator" type="data" format='zip' label="Load a prefitted estimator" />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1011 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1012 </conditional>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1013 <expand macro="feature_selection_SelectFromModel_options"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1014 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1015 </xml>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1016
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1017 <xml name="feature_selection_SelectFromModel_no_prefitted">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1018 <when value="SelectFromModel">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1019 <conditional name="model_inputter">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1020 <param name="input_mode" type="select" label="Construct a new estimator from a selection list?" >
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1021 <option value="new" selected="true">Yes</option>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1022 </param>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1023 <when value="new">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1024 <expand macro="estimator_selector_all"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1025 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1026 </conditional>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1027 <expand macro="feature_selection_SelectFromModel_options"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1028 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1029 </xml>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1030
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1031 <xml name="feature_selection_SelectFromModel_options">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1032 <section name="options" title="Advanced Options" expanded="False">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1033 <param argument="threshold" type="text" value="" optional="true" label="threshold" help="The threshold value to use for feature selection. e.g. 'mean', 'median', '1.25*mean'." />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1034 <param argument="norm_order" type="integer" value="1" label="norm_order" help="Order of the norm used to filter the vectors of coefficients below threshold in the case where the coef_ attribute of the estimator is of dimension 2. " />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1035 <param argument="max_features" type="integer" value="" optional="true" label="The maximum number of features selected scoring above threshold" help="To disable threshold and only select based on max_features, set threshold=-np.inf."/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1036 </section>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1037 </xml>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1038
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1039 <xml name="feature_selection_RFE">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1040 <when value="RFE">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1041 <yield/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1042 <section name="options" title="Advanced Options" expanded="False">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1043 <param argument="n_features_to_select" type="integer" value="" optional="true" label="n_features_to_select" help="The number of features to select. If None, half of the features are selected." />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1044 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1045 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1046 </section>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1047 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1048 </xml>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1049
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1050 <xml name="feature_selection_RFECV">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1051 <when value="RFECV">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1052 <yield/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1053 <section name="options" title="Advanced Options" expanded="False">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1054 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1055 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1056 <expand macro="cv_reduced"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1057 <expand macro="scoring_selection"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1058 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1059 </section>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1060 </when>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1061 </xml>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1062
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1063 <xml name="feature_selection_pipeline">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1064 <!--compare to `feature_selection_fs`, no fitted estimator for SelectFromModel and no customer estimator for RFE and RFECV-->
16
0b57ef8831fb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 15
diff changeset
1065 <conditional name="fs_algorithm_selector">
8
b1c2fe7df3f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 7
diff changeset
1066 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm">
23
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1067 <expand macro="feature_selection_algorithms"/>
8
b1c2fe7df3f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 7
diff changeset
1068 </param>
23
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1069 <expand macro="feature_selection_algorithm_details"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1070 <expand macro="feature_selection_SelectFromModel_no_prefitted"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1071 <expand macro="feature_selection_RFE">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1072 <expand macro="estimator_selector_all"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1073 </expand>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1074 <expand macro="feature_selection_RFECV">
16
0b57ef8831fb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 15
diff changeset
1075 <expand macro="estimator_selector_all"/>
23
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1076 </expand>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1077 </conditional>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1078 </xml>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1079
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1080 <xml name="feature_selection_fs">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1081 <conditional name="fs_algorithm_selector">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1082 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1083 <expand macro="feature_selection_algorithms"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1084 </param>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1085 <expand macro="feature_selection_algorithm_details"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1086 <expand macro="feature_selection_SelectFromModel"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1087 <expand macro="feature_selection_RFE">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1088 <expand macro="estimator_selector_fs"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1089 </expand>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1090 <expand macro="feature_selection_RFECV">
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1091 <expand macro="estimator_selector_fs"/>
75bcb7c19fcf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
1092 </expand>
8
b1c2fe7df3f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 7
diff changeset
1093 </conditional>
b1c2fe7df3f3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 7
diff changeset
1094 </xml>
15
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
1095
6
e44443b071da planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 5
diff changeset
1096 <xml name="feature_selection_score_function">
e44443b071da planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 5
diff changeset
1097 <param argument="score_func" type="select" label="Select a score function">
e44443b071da planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 5
diff changeset
1098 <option value="chi2">chi2 - Compute chi-squared stats between each non-negative feature and class</option>
e44443b071da planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 5
diff changeset
1099 <option value="f_classif">f_classif - Compute the ANOVA F-value for the provided sample</option>
e44443b071da planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 5
diff changeset
1100 <option value="f_regression">f_regression - Univariate linear regression tests</option>
e44443b071da planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 5
diff changeset
1101 <option value="mutual_info_classif">mutual_info_classif - Estimate mutual information for a discrete target variable</option>
e44443b071da planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 5
diff changeset
1102 <option value="mutual_info_regression">mutual_info_regression - Estimate mutual information for a continuous target variable</option>
e44443b071da planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 5
diff changeset
1103 </param>
e44443b071da planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents: 5
diff changeset
1104 </xml>
15
fb232caca397 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 13
diff changeset
1105
7
cdb7948427aa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 6
diff changeset
1106 <xml name="model_validation_common_options">
19
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1107 <expand macro="cv"/>
7
cdb7948427aa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 6
diff changeset
1108 <expand macro="verbose"/>
cdb7948427aa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 6
diff changeset
1109 <yield/>
cdb7948427aa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 6
diff changeset
1110 </xml>
cdb7948427aa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 6
diff changeset
1111
19
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1112 <xml name="scoring_selection">
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1113 <conditional name="scoring">
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1114 <param name="primary_scoring" type="select" multiple="false" label="Select the primary metric (scoring):" help="Metric to refit the best estimator.">
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1115 <option value="default" selected="true">default with estimator</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1116 <option value="accuracy">Classification -- 'accuracy'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1117 <option value="balanced_accuracy">Classification -- 'balanced_accuracy'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1118 <option value="average_precision">Classification -- 'average_precision'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1119 <option value="f1">Classification -- 'f1'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1120 <option value="f1_micro">Classification -- 'f1_micro'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1121 <option value="f1_macro">Classification -- 'f1_macro'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1122 <option value="f1_weighted">Classification -- 'f1_weighted'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1123 <option value="f1_samples">Classification -- 'f1_samples'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1124 <option value="neg_log_loss">Classification -- 'neg_log_loss'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1125 <option value="precision">Classification -- 'precision'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1126 <option value="precision_micro">Classification -- 'precision_micro'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1127 <option value="precision_macro">Classification -- 'precision_macro'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1128 <option value="precision_wighted">Classification -- 'precision_wighted'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1129 <option value="precision_samples">Classification -- 'precision_samples'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1130 <option value="recall">Classification -- 'recall'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1131 <option value="recall_micro">Classification -- 'recall_micro'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1132 <option value="recall_macro">Classification -- 'recall_macro'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1133 <option value="recall_wighted">Classification -- 'recall_wighted'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1134 <option value="recall_samples">Classification -- 'recall_samples'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1135 <option value="roc_auc">Classification -- 'roc_auc'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1136 <option value="explained_variance">Regression -- 'explained_variance'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1137 <option value="neg_mean_absolute_error">Regression -- 'neg_mean_absolute_error'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1138 <option value="neg_mean_squared_error">Regression -- 'neg_mean_squared_error'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1139 <option value="neg_mean_squared_log_error">Regression -- 'neg_mean_squared_log_error'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1140 <option value="neg_median_absolute_error">Regression -- 'neg_median_absolute_error'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1141 <option value="r2">Regression -- 'r2'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1142 </param>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1143 <when value="default"/>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1144 <when value="accuracy"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1145 <when value="balanced_accuracy"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1146 <when value="average_precision"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1147 <when value="f1"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1148 <when value="f1_micro"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1149 <when value="f1_macro"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1150 <when value="f1_weighted"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1151 <when value="f1_samples"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1152 <when value="neg_log_loss"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1153 <when value="precision"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1154 <when value="precision_micro"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1155 <when value="precision_macro"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1156 <when value="precision_wighted"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1157 <when value="precision_samples"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1158 <when value="recall"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1159 <when value="recall_micro"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1160 <when value="recall_macro"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1161 <when value="recall_wighted"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1162 <when value="recall_samples"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1163 <when value="roc_auc"><expand macro="secondary_scoring_selection_classification"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1164 <when value="explained_variance"><expand macro="secondary_scoring_selection_regression"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1165 <when value="neg_mean_absolute_error"><expand macro="secondary_scoring_selection_regression"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1166 <when value="neg_mean_squared_error"><expand macro="secondary_scoring_selection_regression"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1167 <when value="neg_mean_squared_log_error"><expand macro="secondary_scoring_selection_regression"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1168 <when value="neg_median_absolute_error"><expand macro="secondary_scoring_selection_regression"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1169 <when value="r2"><expand macro="secondary_scoring_selection_regression"/></when>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1170 </conditional>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1171 </xml>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1172
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1173 <xml name="secondary_scoring_selection_classification">
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1174 <param name="secondary_scoring" type="select" multiple="true" label="Additional scoring used in multi-metric mode:" help="If the same metric with the primary is chosen, the metric will be ignored.">
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1175 <option value="accuracy">Classification -- 'accuracy'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1176 <option value="balanced_accuracy">Classification -- 'balanced_accuracy'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1177 <option value="average_precision">Classification -- 'average_precision'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1178 <option value="f1">Classification -- 'f1'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1179 <option value="f1_micro">Classification -- 'f1_micro'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1180 <option value="f1_macro">Classification -- 'f1_macro'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1181 <option value="f1_weighted">Classification -- 'f1_weighted'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1182 <option value="f1_samples">Classification -- 'f1_samples'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1183 <option value="neg_log_loss">Classification -- 'neg_log_loss'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1184 <option value="precision">Classification -- 'precision'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1185 <option value="precision_micro">Classification -- 'precision_micro'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1186 <option value="precision_macro">Classification -- 'precision_macro'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1187 <option value="precision_wighted">Classification -- 'precision_wighted'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1188 <option value="precision_samples">Classification -- 'precision_samples'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1189 <option value="recall">Classification -- 'recall'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1190 <option value="recall_micro">Classification -- 'recall_micro'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1191 <option value="recall_macro">Classification -- 'recall_macro'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1192 <option value="recall_wighted">Classification -- 'recall_wighted'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1193 <option value="recall_samples">Classification -- 'recall_samples'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1194 <option value="roc_auc">Classification -- 'roc_auc'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1195 </param>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1196 </xml>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1197
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1198 <xml name="secondary_scoring_selection_regression">
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1199 <param name="secondary_scoring" type="select" multiple="true" label="Additional scoring used in multi-metric mode:" help="If the same metric with the primary is chosen, the metric will be ignored.">
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1200 <option value="explained_variance">Regression -- 'explained_variance'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1201 <option value="neg_mean_absolute_error">Regression -- 'neg_mean_absolute_error'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1202 <option value="neg_mean_squared_error">Regression -- 'neg_mean_squared_error'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1203 <option value="neg_mean_squared_log_error">Regression -- 'neg_mean_squared_log_error'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1204 <option value="neg_median_absolute_error">Regression -- 'neg_median_absolute_error'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1205 <option value="r2">Regression -- 'r2'</option>
98b632c407ae planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 18
diff changeset
1206 </param>
7
cdb7948427aa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 6
diff changeset
1207 </xml>
cdb7948427aa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents: 6
diff changeset
1208