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annotate main_macros.xml @ 2:48ac998ec1b9 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
author bgruening
date Tue, 31 May 2016 16:51:42 -0400
parents a43963a460fb
children dac91f401f4b
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1 <macros>
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2 <token name="@VERSION@">0.9</token>
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3
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4 <xml name="python_requirements">
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5 <requirements>
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6 <requirement type="package" version="0.2.1b">eden</requirement>
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7 <yield />
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8 </requirements>
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9 </xml>
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10
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11 <xml name="macro_stdio">
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12 <stdio>
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13 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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14 </stdio>
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15 </xml>
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16
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17
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18 <!--Generic interface-->
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19 <xml name="train_loadConditional" token_train="tabular" token_data="tabular" token_model="txt">
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20 <conditional name="selected_tasks">
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21 <param name="selected_task" type="select" label="Select a Classification Task">
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22 <option value="train" selected="true">Train a model</option>
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23 <option value="load">Load a model and predict</option>
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24 </param>
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25 <when value="load">
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26 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file." />
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27 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
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28 <conditional name="prediction_options">
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29 <param name="prediction_option" type="select" label="Select the type of prediction">
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30 <option value="predict">Predict class labels</option>
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31 <option value="advanced">Include advanced options</option>
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32 </param>
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33 <when value="predict">
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34 </when>
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35 <when value="advanced">
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36 </when>
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37 </conditional>
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38 </when>
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39 <when value="train">
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40 <param name="infile_train" type="data" format="@TRAIN@" label="Training samples (tabular)" />
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41 <conditional name="selected_algorithms">
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42 <yield />
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43 </conditional>
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44 </when>
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45 </conditional>
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46 </xml>
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47
2
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48 <xml name="sl_Conditional" token_train="tabular" token_data="tabular" token_model="txt">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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49 <conditional name="selected_tasks">
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50 <param name="selected_task" type="select" label="Select a Classification Task">
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51 <option value="train" selected="true">Train a model</option>
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52 <option value="load">Load a model and predict</option>
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53 </param>
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54 <when value="load">
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55 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file." />
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56 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
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57 <conditional name="prediction_options">
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58 <param name="prediction_option" type="select" label="Select the type of prediction">
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59 <option value="predict">Predict class labels</option>
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60 <option value="advanced">Include advanced options</option>
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61 </param>
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62 <when value="predict">
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63 </when>
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64 <when value="advanced">
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65 </when>
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66 </conditional>
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67 </when>
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68 <when value="train">
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69 <conditional name="selected_algorithms">
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70 <yield />
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71 </conditional>
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72 </when>
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73 </conditional>
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74 </xml>
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75
0
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76 <xml name="advanced_section">
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77 <section name="options" title="Advanced Options" expanded="False">
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78 <yield />
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79 </section>
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80 </xml>
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81
2
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82
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83 <!--Ensemble methods-->
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84 <xml name="n_estimators" token_default_value="10" token_help=" ">
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85 <param argument="n_estimators" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of trees in the forest" help="@HELP@"/>
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86 </xml>
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87
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88 <xml name="max_depth" token_default_value="" token_help=" ">
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89 <param argument="max_depth" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@"/>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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90 </xml>
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92 <xml name="min_samples_split" token_default_value="2" token_help=" ">
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93 <param argument="min_samples_split" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@"/>
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94 </xml>
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95
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96 <xml name="min_samples_leaf" token_default_value="1" token_help=" ">
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97 <param argument="min_samples_leaf" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Minimum number of samples in newly created leaves" help="@HELP@"/>
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98 </xml>
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99
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100 <xml name="min_weight_fraction_leaf" token_default_value="0.0" token_help=" ">
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101 <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@"/>
0
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102 </xml>
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103
2
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104 <xml name="max_leaf_nodes" token_default_value="" token_help=" ">
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105 <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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106 </xml>
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107
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108 <xml name="bootstrap" token_checked="true" token_help=" ">
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109 <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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110 </xml>
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111
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112 <xml name="criterion" token_help=" ">
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113 <param argument="criterion" type="select" label="Function to measure the quality of a split" help=" ">
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114 <option value="gini" selected="true">Gini impurity</option>
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115 <option value="entropy">Information gain</option>
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116 <yield/>
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117 </param>
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118 </xml>
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119
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120 <xml name="oob_score" token_checked="flase" token_help=" ">
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121 <param argument="oob_score" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Use out-of-bag samples to estimate the generalization error" help="@HELP@"/>
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122 </xml>
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123
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124 <xml name="max_features" token_default_value="auto" token_help="This could be an integer, float, string, or None. For more information please refer to help. ">
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125 <param argument="max_features" type="text" optional="true" value="@DEFAULT_VALUE@" label="Number of features for finding the best split" help="@HELP@"/>
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126 </xml>
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127
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128 <xml name="learning_rate" token_default_value="1.0" token_help=" ">
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129 <param argument="learning_rate" type="float" optional="true" value="@DEFAULT_VALUE@" label="Learning rate" help="@HELP@"/>
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130 </xml>
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131
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132
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133 <!--Parameters-->
0
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134 <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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135 <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@"/>
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136 </xml>
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137
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138 <xml name="n_clusters" token_default_value="8">
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139 <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" "/>
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140 </xml>
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141
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142 <xml name="fit_intercept" token_checked="true">
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143 <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Estimate the intercept" help="If false, the data is assumed to be already centered."/>
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144 </xml>
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145
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146 <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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147 <param argument="n_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@"/>
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148 </xml>
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149
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150 <xml name="shuffle" token_checked="true" token_help_text=" " token_label="Shuffle data after each iteration">
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151 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="@LABEL@" help="@HELP_TEXT@"/>
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152 </xml>
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153
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154 <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.">
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155 <param argument="random_state" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Random seed number" help="@HELP_TEXT@"/>
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156 </xml>
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157
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158 <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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159 <param argument="warm_start" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Perform warm start" help="@HELP_TEXT@"/>
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160 </xml>
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161
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162 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term.">
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163 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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164 </xml>
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165
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166 <!--xml name="class_weight" token_default_value="" token_help_text="">
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167 <param argument="class_weight" type="" optional="true" value="@DEFAULT_VALUE@" label="" help="@HELP_TEXT@"/>
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168 </xml-->
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169
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170 <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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171 <param argument="alpha" type="float" optional="true" value="@DEFAULT_VALUE@" label="Regularization coefficient" help="@HELP_TEXT@"/>
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172 </xml>
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173
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174 <xml name="n_samples" token_default_value="100" token_help_text="The total number of points equally divided among clusters.">
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175 <param argument="n_samples" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of samples" help="@HELP_TEXT@"/>
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176 </xml>
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177
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178 <xml name="n_features" token_default_value="2" token_help_text="Number of different numerical properties produced for each sample.">
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179 <param argument="n_features" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of features" help="@HELP_TEXT@"/>
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180 </xml>
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181
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182 <xml name="noise" token_default_value="0.0" token_help_text="Floating point number. ">
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183 <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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184 </xml>
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185
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186 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term. ">
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187 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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188 </xml>
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189
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190 <xml name="max_iter" token_default_value="300" token_label="Maximum number of iterations per single run" token_help_text=" ">
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191 <param argument="max_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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192 </xml>
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193
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194 <xml name="n_init" token_default_value="10" >
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195 <param argument="n_init" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of runs with different centroid seeds" help=" "/>
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196 </xml>
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197
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198 <xml name="init">
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199 <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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200 <option value="k-means++">k-means++</option>
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201 <option value="random">random</option>
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202 </param>
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203 </xml>
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204
1
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205 <xml name="gamma" token_default_value="1.0" token_label="Scaling parameter" token_help_text=" ">
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206 <param argument="gamma" type="float" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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207 </xml>
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208
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209 <xml name="degree" token_default_value="3" token_label="Degree of the polynomial" token_help_text=" ">
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210 <param argument="degree" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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211 </xml>
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212
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213 <xml name="coef0" token_default_value="1" token_label="Zero coefficient" token_help_text=" ">
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214 <param argument="coef0" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
2
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215 </xml>
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216
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217 <xml name="pos_label" token_default_value="">
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218 <param argument="pos_label" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Label of the positive class" help=" "/>
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219 </xml>
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220
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221 <xml name="average">
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222 <param argument="average" type="select" optional="True" label="Averaging type" help=" ">
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223 <option value="binary" selected="true" help="Only report results for the class specified by pos_label. Applicable only on binary classification.">binary</option>
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224 <option value="micro" help="Calculate metrics globally by counting the total true positives, false negatives and false positives.">micro</option>
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225 <option value="samples" help="Calculate metrics for each instance, and find their average (only meaningful for multilabel).">samples</option>
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226 <!--option value="macro" help=""></option-->
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227 <!--option value="weighted" help=""></option-->
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228 </param>
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229 </xml>
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230
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231 <xml name="beta">
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232 <param argument="beta" type="float" value="1.0" label="The strength of recall versus precision in the F-score" help=" "/>
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233 </xml>
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234
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235
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236 <!--Data interface-->
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237 <xml name="tabular_input">
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238 <param name="infile" type="data" format="tabular" label="Data file with numeric values"/>
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239 <param name="start_column" type="data_column" data_ref="infile" optional="True" label="Select a subset of data. Start column:" />
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240 <param name="end_column" type="data_column" data_ref="infile" optional="True" label="End column:" />
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241 </xml>
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242
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243 <xml name="sample_cols" token_label1="File containing true class labels:" token_label2="File containing predicted class labels:" token_multiple1="False" token_multiple2="False" token_format1="tabular" token_format2="tabular" token_help1="" token_help2="">
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244 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
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245 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/>
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246 <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/>
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247 <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
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248 <yield/>
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249 </xml>
1
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250
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251 <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.">
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252 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):">
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253 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/>
0
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254 </repeat>
2
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255 </xml>
0
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256
2
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257 <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="">
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258 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
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259 <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/>
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260 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
0
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261 </xml>
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262
2
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263 <xml name="sl_mixed_input">
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264 <conditional name="input_options">
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265 <param name="selected_input" type="select" label="Select input type:">
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266 <option value="tabular" selected="true">tabular data</option>
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267 <option value="sparse">sparse matrix</option>
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268 </param>
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269 <when value="tabular">
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270 <expand macro="sample_cols" multiple1="true"/>
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271 </when>
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272 <when value="sparse">
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273 <expand macro="sparse_target"/>
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274 </when>
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275 </conditional>
0
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276 </xml>
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277
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278
2
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279 <!--Advanced options-->
0
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280 <xml name="nn_advanced_options">
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281 <section name="options" title="Advanced Options" expanded="False">
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282 <yield/>
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283 <param argument="weights" type="select" label="Weight function" help="Used in prediction.">
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284 <option value="uniform" selected="true" help="Uniform weights. All points in each neighborhood are weighted equally.">Uniform</option>
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285 <option value="distance" help="Weight points by the inverse of their distance.">Distance</option>
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286 </param>
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287 <param argument="algorithm" type="select" label="Neighbor selection algorithm" help=" ">
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288 <option value="auto" selected="true">Auto</option>
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289 <option value="ball_tree">BallTree</option>
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290 <option value="kd_tree">KDTree</option>
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291 <option value="brute">Brute-force</option>
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292 </param>
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293 <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."/>
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294 <!--param name="metric"-->
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295 <!--param name="p"-->
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296 <!--param name="metric_params"-->
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297 </section>
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298 </xml>
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299
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300 <xml name="svc_advanced_options">
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301 <section name="options" title="Advanced Options" expanded="False">
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302 <yield/>
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303 <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.">
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304 <option value="rbf" selected="true">rbf</option>
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305 <option value="linear">linear</option>
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306 <option value="poly">poly</option>
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307 <option value="sigmoid">sigmoid</option>
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308 <option value="precomputed">precomputed</option>
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309 </param>
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310 <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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311 <!--TODO: param argument="gamma" float, optional (default=’auto’) -->
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312 <param argument="coef0" type="float" optional="true" value="0.0" label="Zero coefficient (polynomial and sigmoid kernels only)" help="Independent term in kernel function. dafault: 0.0 "/>
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313 <param argument="shrinking" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use the shrinking heuristic" help=" "/>
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314 <param argument="probability" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Enable probability estimates. " help="This must be enabled prior to calling fit, and will slow down that method."/>
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315 <!-- param argument="cache_size"-->
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316 <!--expand macro="class_weight"/-->
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317 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. "/>
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318 <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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319 <!--param argument="decision_function_shape"-->
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320 <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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321 </section>
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322 </xml>
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323
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324 <xml name="spectral_clustering_advanced_options">
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325 <section name="options" title="Advanced Options" expanded="False">
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326 <expand macro="n_clusters"/>
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327 <param argument="eigen_solver" type="select" value="" label="Eigen solver" help="The eigenvalue decomposition strategy to use.">
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328 <option value="arpack" selected="true">arpack</option>
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329 <option value="lobpcg">lobpcg</option>
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330 <option value="amg">amg</option>
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331 <!--None-->
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332 </param>
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333 <expand macro="random_state"/>
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334 <expand macro="n_init"/>
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335 <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''."/>
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336 <param argument="affinity" type="select" label="Affinity" help="Affinity kernel to use. ">
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337 <option value="rbf" selected="true">RBF</option>
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338 <option value="precomputed">precomputed</option>
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339 <option value="nearest_neighbors">Nearset neighbors</option>
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340 </param>
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341 <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''"/>
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342 <!--param argument="eigen_tol"-->
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343 <param argument="assign_labels" type="select" label="Assign labels" help="The strategy to use to assign labels in the embedding space.">
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344 <option value="kmeans" selected="true">kmeans</option>
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345 <option value="discretize">discretize</option>
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346 </param>
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347 <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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348 <param argument="coef0" type="integer" optional="true" value="1" label="Zero coefficient (polynomial and sigmoid kernels only)" help="Ignored by other kernels. dafault : 1 "/>
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349 <!--param argument="kernel_params"-->
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350 </section>
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351 </xml>
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352
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353 <xml name="minibatch_kmeans_advanced_options">
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354 <section name="options" title="Advanced Options" expanded="False">
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355 <expand macro="n_clusters"/>
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356 <expand macro="init"/>
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357 <expand macro="n_init" default_value="3"/>
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358 <expand macro="max_iter" default_value="100"/>
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359 <expand macro="tol" help_text="Early stopping heuristics based on normalized center change. To disable set to 0.0 ."/>
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360 <expand macro="random_state"/>
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361 <param argument="batch_size" type="integer" optional="true" value="100" label="Batch size" help="Size of the mini batches."/>
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362 <!--param argument="compute_labels"-->
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363 <param argument="max_no_improvement" type="integer" optional="true" value="10" label="Maximum number of improvement attempts" help="
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364 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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365 To disable, set max_no_improvement to None. "/>
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366 <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 )"/>
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367 <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."/>
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368 </section>
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369 </xml>
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370
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371 <xml name="kmeans_advanced_options">
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372 <section name="options" title="Advanced Options" expanded="False">
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373 <expand macro="n_clusters"/>
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374 <expand macro="init"/>
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375 <expand macro="n_init"/>
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376 <expand macro="max_iter"/>
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377 <expand macro="tol" default_value="0.0001" help_text="Relative tolerance with regards to inertia to declare convergence."/>
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378 <!--param argument="precompute_distances"/-->
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379 <expand macro="random_state"/>
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380 <param argument="copy_x" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" 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."/>
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381 </section>
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382 </xml>
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383
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384 <xml name="birch_advanced_options">
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385 <section name="options" title="Advanced Options" expanded="False">
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386 <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."/>
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387 <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."/>
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388 <expand macro="n_clusters" default_value="3"/>
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389 <!--param argument="compute_labels"/-->
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390 </section>
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391 </xml>
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392
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393 <xml name="dbscan_advanced_options">
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394 <section name="options" title="Advanced Options" expanded="False">
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395 <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."/>
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396 <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."/>
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397 <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."/>
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398 <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.">
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399 <option value="auto" selected="true">auto</option>
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400 <option value="ball_tree">ball_tree</option>
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401 <option value="kd_tree">kd_tree</option>
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402 <option value="brute">brute</option>
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403 </param>
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404 <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."/>
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405 </section>
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406 </xml>
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407
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408 <xml name="clustering_algorithms_options">
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409 <conditional name="algorithm_options">
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410 <param name="selected_algorithm" type="select" label="Clustering Algorithm">
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411 <option value="KMeans" selected="true">KMeans</option>
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412 <option value="SpectralClustering">Spectral Clustering</option>
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413 <option value="MiniBatchKMeans">Mini Batch KMeans</option>
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414 <option value="DBSCAN">DBSCAN</option>
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415 <option value="Birch">Birch</option>
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416 </param>
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417 <when value="KMeans">
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418 <expand macro="kmeans_advanced_options"/>
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419 </when>
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420 <when value="DBSCAN">
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421 <expand macro="dbscan_advanced_options"/>
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422 </when>
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423 <when value="Birch">
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424 <expand macro="birch_advanced_options"/>
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425 </when>
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426 <when value="SpectralClustering">
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427 <expand macro="spectral_clustering_advanced_options"/>
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428 </when>
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429 <when value="MiniBatchKMeans">
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430 <expand macro="minibatch_kmeans_advanced_options"/>
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431 </when>
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432 </conditional>
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433 </xml>
1
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434
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435 <xml name="distance_metrics">
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436 <param argument="metric" type="select" label="Distance metric" help=" ">
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437 <option value="euclidean" selected="true">euclidean</option>
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438 <option value="cityblock">cityblock</option>
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439 <option value="cosine">cosine</option>
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440 <option value="l1">l1</option>
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441 <option value="l2">l2</option>
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442 <option value="manhattan">manhattan</option>
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443 <yield/>
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444 </param>
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445 </xml>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
446
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
447 <xml name="distance_nonsparse_metrics">
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
448 <option value="braycurtis">braycurtis</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
449 <option value="canberra">canberra</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
450 <option value="chebyshev">chebyshev</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
451 <option value="correlation">correlation</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
452 <option value="dice">dice</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
453 <option value="hamming">hamming</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
454 <option value="jaccard">jaccard</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
455 <option value="kulsinski">kulsinski</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
456 <option value="mahalanobis">mahalanobis</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
457 <option value="matching">matching</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
458 <option value="minkowski">minkowski</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
459 <option value="rogerstanimoto">rogerstanimoto</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
460 <option value="russellrao">russellrao</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
461 <option value="seuclidean">seuclidean</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
462 <option value="sokalmichener">sokalmichener</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
463 <option value="sokalsneath">sokalsneath</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
464 <option value="sqeuclidean">sqeuclidean</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
465 <option value="yule">yule</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
466 </xml>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
467
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
468 <xml name="pairwise_kernel_metrics">
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
469 <param argument="metric" type="select" label="Pirwise Kernel metric" help=" ">
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
470 <option value="rbf" selected="true">rbf</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
471 <option value="sigmoid">sigmoid</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
472 <option value="polynomial">polynomial</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
473 <option value="linear" selected="true">linear</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
474 <option value="chi2">chi2</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
475 <option value="additive_chi2">additive_chi2</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
476 </param>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
477 </xml>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
478
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
479 <xml name="sparse_pairwise_metric_functions">
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
480 <param name="selected_metric_function" type="select" label="Select the pairwise metric you want to compute:">
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
481 <option value="euclidean_distances" selected="true">Euclidean distance matrix</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
482 <option value="pairwise_distances">Distance matrix</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
483 <option value="pairwise_distances_argmin">Minimum distances between one point and a set of points</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
484 <yield/>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
485 </param>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
486 </xml>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
487
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
488 <xml name="pairwise_metric_functions">
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
489 <option value="additive_chi2_kernel" >Additive chi-squared kernel</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
490 <option value="chi2_kernel">Exponential chi-squared kernel</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
491 <option value="linear_kernel">Linear kernel</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
492 <option value="manhattan_distances">L1 distances</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
493 <option value="pairwise_kernels">Kernel</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
494 <option value="polynomial_kernel">Polynomial kernel</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
495 <option value="rbf_kernel">Gaussian (rbf) kernel</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
496 <option value="laplacian_kernel">Laplacian kernel</option>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
497 </xml>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
498
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
499 <xml name="sparse_pairwise_condition">
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
500 <when value="pairwise_distances">
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
501 <section name="options" title="Advanced Options" expanded="False">
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
502 <expand macro="distance_metrics">
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
503 <yield/>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
504 </expand>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
505 </section>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
506 </when>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
507 <when value="euclidean_distances">
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
508 <section name="options" title="Advanced Options" expanded="False">
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
509 <param argument="squared" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Return squared Euclidean distances" help=" "/>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
510 </section>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
511 </when>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
512 </xml>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
513
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
514 <xml name="argmin_distance_condition">
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
515 <when value="pairwise_distances_argmin">
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
516 <section name="options" title="Advanced Options" expanded="False">
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
517 <param argument="axis" type="integer" optional="true" value="1" label="Axis" help="Axis along which the argmin and distances are to be computed."/>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
518 <expand macro="distance_metrics">
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
519 <yield/>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
520 </expand>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
521 <param argument="batch_size" type="integer" optional="true" value="500" label="Batch size" help="Number of rows to be processed in each batch run."/>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
522 </section>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
523 </when>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
524 </xml>
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
525
2
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
526 <xml name="sparse_preprocessors">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
527 <param name="selected_pre_processor" type="select" label="Select a preprocessor:">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
528 <option value="StandardScaler" selected="true">Standardize features by removing the mean and scaling to unit variance</option>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
529 <option value="Binarizer">Binarize data</option>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
530 <option value="Imputer">Complete missing values</option>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
531 <option value="MaxAbsScaler">Scale features by their maximum absolute value</option>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
532 <option value="Normalizer">Normalize samples individually to unit norm</option>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
533 <yield/>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
534 </param>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
535 </xml>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
536
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
537 <xml name="sparse_preprocessor_options">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
538 <when value="Binarizer">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
539 <section name="options" title="Advanced Options" expanded="False">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
540 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing binarization" help=" "/>
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541 <param argument="threshold" type="float" optional="true" value="0.0" label="Threshold" 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. "/>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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542 </section>
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543 </when>
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544 <when value="Imputer">
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545 <section name="options" title="Advanced Options" expanded="False">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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546 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing imputation" help=" "/>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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547 <param argument="strategy" type="select" optional="true" label="Imputation strategy" help=" ">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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548 <option value="mean" selected="true">Replace missing values using the mean along the axis</option>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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549 <option value="median">Replace missing values using the median along the axis</option>
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550 <option value="most_frequent">Replace missing using the most frequent value along the axis</option>
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551 </param>
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552 <param argument="missing_values" type="text" optional="true" value="NaN" label="Placeholder for missing values" help="For missing values encoded as numpy.nan, use the string value “NaN”"/>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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553 <param argument="axis" type="select" optional="true" label="The axis along which to impute" help=" ">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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554 <option value="0" selected="true">Impute along columns</option>
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555 <option value="1">Impute along rows</option>
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556 </param>
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557 </section>
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558 </when>
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559 <when value="StandardScaler">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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560 <section name="options" title="Advanced Options" expanded="False">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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561 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for performing inplace scaling" help=" "/>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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562 <param argument="with_mean" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Center the data before scaling" help=" "/>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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563 <param argument="with_std" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Scale the data to unit variance (or unit standard deviation)" help=" "/>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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564 </section>
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565 </when>
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566 <when value="MaxAbsScaler">
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567 <section name="options" title="Advanced Options" expanded="False">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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568 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing scaling" help=" "/>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
569 </section>
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570 </when>
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571 <when value="Normalizer">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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572 <section name="options" title="Advanced Options" expanded="False">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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573 <param argument="norm" type="select" optional="true" label="The norm to use to normalize non zero samples" help=" ">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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574 <option value="l1" selected="true">l1</option>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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575 <option value="l2">l2</option>
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576 <option value="max">max</option>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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577 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing row normalization" help=" "/>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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578 </param>
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diff changeset
579 </section>
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580 </when>
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diff changeset
581 <yield/>
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diff changeset
582 </xml>
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583
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584
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585 <!--Citations-->
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586 <xml name="eden_citation">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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587 <citations>
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588 <citation type="bibtex">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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589 @misc{fabrizio_costa_2015_15094,
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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590 author = {Fabrizio Costa and
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591 Björn Grüning and
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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592 gigolo},
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593 title = {EDeN: EDeN - Graph Vectorizer},
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594 month = feb,
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595 year = 2015,
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596 doi = {10.5281/zenodo.15094},
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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597 url = {http://dx.doi.org/10.5281/zenodo.15094}
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598 }
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599 }
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600 </citation>
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601 </citations>
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602 </xml>
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603
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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604 <xml name="sklearn_citation">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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605 <citations>
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606 <citation type="bibtex">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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607 @article{scikit-learn,
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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608 title={Scikit-learn: Machine Learning in {P}ython},
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609 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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610 and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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611 and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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612 Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
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613 journal={Journal of Machine Learning Research},
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614 volume={12},
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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615 pages={2825--2830},
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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616 year={2011}
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617 url = {https://github.com/scikit-learn/scikit-learn}
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618 }
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619 </citation>
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620 </citations>
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diff changeset
621 </xml>
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622
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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623 <xml name="scipy_citation">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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624 <citations>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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625 <citation type="bibtex">
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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626 @Misc{,
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627 author = {Eric Jones and Travis Oliphant and Pearu Peterson and others},
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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628 title = {{SciPy}: Open source scientific tools for {Python}},
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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629 year = {2001--},
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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630 url = "http://www.scipy.org/",
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631 note = {[Online; accessed 2016-04-09]}
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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632 }
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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633 </citation>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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634 </citations>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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635 </xml>
48ac998ec1b9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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636
1
a43963a460fb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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637 </macros>