Mercurial > repos > bgruening > sklearn_discriminant_classifier

annotate main_macros.xml @ 5:8e489f4ff47c draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
author bgruening
date Tue, 10 Apr 2018 15:19:43 -0400
parents 76fc0cd26c5c
children e44443b071da
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e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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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 <token name="@COLUMNS_FUNCTION@">
2
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5 def read_columns(f, c, **args):
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6 data = pandas.read_csv(f, **args)
0
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7 cols = c.split (',')
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8 cols = map(int, cols)
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9 cols = list(map(lambda x: x - 1, cols))
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10 y = data.iloc[:,cols].values
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11 return y
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12 </token>
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13
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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14 <xml name="python_requirements">
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15 <requirements>
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16 <requirement type="package" version="2.7">python</requirement>
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17 <requirement type="package" version="0.19.1">scikit-learn</requirement>
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18 <requirement type="package" version="0.22.0">pandas</requirement>
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19 <yield />
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20 </requirements>
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21 </xml>
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22
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23 <xml name="macro_stdio">
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24 <stdio>
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25 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
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26 </stdio>
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27 </xml>
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28
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29
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30 <!--Generic interface-->
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31 <xml name="train_loadConditional" token_train="tabular" token_data="tabular" token_model="txt">
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32 <conditional name="selected_tasks">
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33 <param name="selected_task" type="select" label="Select a Classification Task">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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34 <option value="train" selected="true">Train a model</option>
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35 <option value="load">Load a model and predict</option>
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36 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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37 <when value="load">
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38 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/>
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39 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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40 <conditional name="prediction_options">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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41 <param name="prediction_option" type="select" label="Select the type of prediction">
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42 <option value="predict">Predict class labels</option>
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43 <option value="advanced">Include advanced options</option>
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44 </param>
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45 <when value="predict">
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46 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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47 <when value="advanced">
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48 </when>
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49 </conditional>
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50 </when>
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51 <when value="train">
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52 <param name="infile_train" type="data" format="@TRAIN@" label="Training samples (tabular)"/>
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53 <conditional name="selected_algorithms">
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54 <yield />
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55 </conditional>
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56 </when>
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57 </conditional>
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58 </xml>
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59
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60 <xml name="sl_Conditional" token_train="tabular" token_data="tabular" token_model="txt">
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61 <conditional name="selected_tasks">
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62 <param name="selected_task" type="select" label="Select a Classification Task">
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63 <option value="train" selected="true">Train a model</option>
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64 <option value="load">Load a model and predict</option>
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65 </param>
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66 <when value="load">
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67 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/>
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68 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
5
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69 <param name="header" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
0
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70 <conditional name="prediction_options">
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71 <param name="prediction_option" type="select" label="Select the type of prediction">
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72 <option value="predict">Predict class labels</option>
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73 <option value="advanced">Include advanced options</option>
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74 </param>
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75 <when value="predict">
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76 </when>
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77 <when value="advanced">
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78 </when>
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79 </conditional>
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80 </when>
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81 <when value="train">
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82 <conditional name="selected_algorithms">
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83 <yield />
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84 </conditional>
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85 </when>
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86 </conditional>
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87 </xml>
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88
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89 <xml name="advanced_section">
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90 <section name="options" title="Advanced Options" expanded="False">
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91 <yield />
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92 </section>
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93 </xml>
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94
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95
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96 <!--Generalized Linear Models-->
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97 <xml name="loss" token_help=" " token_select="false">
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98 <param argument="loss" type="select" label="Loss function" help="@HELP@">
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99 <option value="squared_loss" selected="@SELECT@">squared loss</option>
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100 <option value="huber">huber</option>
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101 <option value="epsilon_insensitive">epsilon insensitive</option>
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102 <option value="squared_epsilon_insensitive">squared epsilon insensitive</option>
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103 <yield/>
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104 </param>
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105 </xml>
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106
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107 <xml name="penalty" token_help=" ">
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108 <param argument="penalty" type="select" label="Penalty (regularization term)" help="@HELP@">
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109 <option value="l2" selected="true">l2</option>
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110 <option value="l1">l1</option>
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111 <option value="elasticnet">elastic net</option>
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112 <option value="none">none</option>
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113 <yield/>
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114 </param>
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115 </xml>
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116
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117 <xml name="l1_ratio" token_default_value="0.15" token_help=" ">
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118 <param argument="l1_ratio" type="float" value="@DEFAULT_VALUE@" label="Elastic Net mixing parameter" help="@HELP@"/>
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119 </xml>
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120
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121 <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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122 <param argument="epsilon" type="float" value="@DEFAULT_VALUE@" label="Epsilon (epsilon-sensitive loss functions only)" help="@HELP@"/>
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123 </xml>
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124
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125 <xml name="learning_rate_s" token_help=" " token_selected1="false" token_selected2="false">
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126 <param argument="learning_rate" type="select" optional="true" label="Learning rate schedule" help="@HELP@">
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127 <option value="optimal" selected="@SELECTED1@">optimal</option>
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128 <option value="constant">constant</option>
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129 <option value="invscaling" selected="@SELECTED2@">inverse scaling</option>
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130 <yield/>
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131 </param>
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132 </xml>
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133
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134 <xml name="eta0" token_default_value="0.0" token_help="Used with ‘constant’ or ‘invscaling’ schedules. ">
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135 <param argument="eta0" type="float" value="@DEFAULT_VALUE@" label="Initial learning rate" help="@HELP@"/>
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136 </xml>
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137
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138 <xml name="power_t" token_default_value="0.5" token_help=" ">
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139 <param argument="power_t" type="float" value="@DEFAULT_VALUE@" label="Exponent for inverse scaling learning rate" help="@HELP@"/>
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140 </xml>
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141
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142 <xml name="normalize" token_checked="false" token_help=" ">
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143 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Normalize samples before training" help=" "/>
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144 </xml>
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145
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146 <xml name="copy_X" token_checked="true" token_help=" ">
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147 <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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148 </xml>
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149
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150 <xml name="ridge_params">
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151 <expand macro="normalize"/>
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152 <expand macro="alpha" default_value="1.0"/>
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153 <expand macro="fit_intercept"/>
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154 <expand macro="max_iter" default_value=""/>
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155 <expand macro="tol" default_value="0.001" help_text="Precision of the solution. "/>
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156 <!--class_weight-->
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157 <expand macro="copy_X"/>
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158 <param argument="solver" type="select" value="" label="Solver to use in the computational routines" help=" ">
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159 <option value="auto" selected="true">auto</option>
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160 <option value="svd">svd</option>
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161 <option value="cholesky">cholesky</option>
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162 <option value="lsqr">lsqr</option>
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163 <option value="sparse_cg">sparse_cg</option>
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164 <option value="sag">sag</option>
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165 </param>
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166 <expand macro="random_state"/>
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167 </xml>
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168
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169 <!--Ensemble methods-->
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170 <xml name="n_estimators" token_default_value="10" token_help=" ">
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171 <param argument="n_estimators" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of trees in the forest" help="@HELP@"/>
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172 </xml>
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173
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174 <xml name="max_depth" token_default_value="" token_help=" ">
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175 <param argument="max_depth" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@"/>
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176 </xml>
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177
5
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178 <xml name="min_samples_split" token_type="integer" token_default_value="2" token_help=" ">
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179 <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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180 </xml>
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181
5
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182 <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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183 <param argument="min_samples_leaf" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP@"/>
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184 </xml>
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185
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186 <xml name="min_weight_fraction_leaf" token_default_value="0.0" token_help=" ">
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187 <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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188 </xml>
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189
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190 <xml name="max_leaf_nodes" token_default_value="" token_help=" ">
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191 <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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192 </xml>
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193
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194 <xml name="min_impurity_decrease" token_default_value="0" token_help=" ">
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195 <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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196 </xml>
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197
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198 <xml name="bootstrap" token_checked="true" token_help=" ">
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199 <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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200 </xml>
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201
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202 <xml name="criterion" token_help=" ">
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203 <param argument="criterion" type="select" label="Function to measure the quality of a split" help=" ">
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204 <option value="gini" selected="true">Gini impurity</option>
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205 <option value="entropy">Information gain</option>
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206 <yield/>
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207 </param>
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208 </xml>
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209
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210 <xml name="criterion2" token_help="">
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211 <param argument="criterion" type="select" label="Function to measure the quality of a split" >
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212 <option value="mse">mse - mean squared error</option>
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213 <option value="mae">mae - mean absolute error</option>
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214 <yield/>
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215 </param>
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216 </xml>
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217
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218 <xml name="oob_score" token_checked="false" token_help=" ">
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219 <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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220 </xml>
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221
5
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222 <xml name="max_features">
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223 <conditional name="select_max_features">
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224 <param argument="max_features" type="select" label="max_features">
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225 <option value="auto" selected="true">auto - max_features=n_features</option>
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226 <option value="sqrt">sqrt - max_features=sqrt(n_features)</option>
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227 <option value="log2">log2 - max_features=log2(n_features)</option>
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228 <option value="number_input">I want to type the number in or input None type</option>
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229 </param>
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230 <when value="auto">
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231 </when>
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232 <when value="sqrt">
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233 </when>
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234 <when value="log2">
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235 </when>
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236 <when value="number_input">
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237 <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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238 </when>
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239 </conditional>
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240 </xml>
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241
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242 <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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243 <param argument="verbose" type="integer" value="@DEFAULT_VALUE@" optional="true" label="Enable verbose output" help="@HELP@"/>
0
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244 </xml>
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245
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246 <xml name="learning_rate" token_default_value="1.0" token_help=" ">
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247 <param argument="learning_rate" type="float" optional="true" value="@DEFAULT_VALUE@" label="Learning rate" help="@HELP@"/>
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248 </xml>
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249
5
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250 <xml name="subsample" token_help=" ">
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251 <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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252 </xml>
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253
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254 <xml name="presort">
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255 <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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256 <option value="auto" selected="true">auto</option>
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257 <option value="true">true</option>
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258 <option value="false">false</option>
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259 </param>
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260 </xml>
0
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261
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262 <!--Parameters-->
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263 <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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264 <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@"/>
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265 </xml>
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266
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267 <xml name="n_clusters" token_default_value="8">
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268 <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" "/>
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269 </xml>
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270
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271 <xml name="fit_intercept" token_checked="true">
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272 <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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273 </xml>
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274
5
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275 <xml name="n_jobs" token_default_value="1" token_label="The number of jobs to run in parallel for both fit and predict">
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276 <param argument="n_jobs" type="integer" value="@DEFAULT_VALUE@" optional="true" label="@LABEL@" help="If -1, then the number of jobs is set to the number of cores"/>
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277 </xml>
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278
0
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279 <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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280 <param argument="n_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@"/>
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281 </xml>
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282
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283 <xml name="shuffle" token_checked="true" token_help_text=" " token_label="Shuffle data after each iteration">
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284 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="@LABEL@" help="@HELP_TEXT@"/>
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285 </xml>
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286
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287 <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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288 <param argument="random_state" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Random seed number" help="@HELP_TEXT@"/>
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289 </xml>
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290
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291 <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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292 <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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293 </xml>
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294
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295 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term.">
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296 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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297 </xml>
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298
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299 <!--xml name="class_weight" token_default_value="" token_help_text="">
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300 <param argument="class_weight" type="" optional="true" value="@DEFAULT_VALUE@" label="" help="@HELP_TEXT@"/>
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301 </xml-->
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302
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303 <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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304 <param argument="alpha" type="float" optional="true" value="@DEFAULT_VALUE@" label="Regularization coefficient" help="@HELP_TEXT@"/>
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305 </xml>
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306
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307 <xml name="n_samples" token_default_value="100" token_help_text="The total number of points equally divided among clusters.">
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308 <param argument="n_samples" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of samples" help="@HELP_TEXT@"/>
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309 </xml>
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310
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311 <xml name="n_features" token_default_value="2" token_help_text="Number of different numerical properties produced for each sample.">
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312 <param argument="n_features" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of features" help="@HELP_TEXT@"/>
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313 </xml>
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314
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315 <xml name="noise" token_default_value="0.0" token_help_text="Floating point number. ">
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316 <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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317 </xml>
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318
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319 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term. ">
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320 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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321 </xml>
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322
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323 <xml name="max_iter" token_default_value="300" token_label="Maximum number of iterations per single run" token_help_text=" ">
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324 <param argument="max_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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325 </xml>
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326
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327 <xml name="n_init" token_default_value="10" >
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328 <param argument="n_init" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of runs with different centroid seeds" help=" "/>
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329 </xml>
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330
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331 <xml name="init">
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332 <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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333 <option value="k-means++">k-means++</option>
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334 <option value="random">random</option>
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335 </param>
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336 </xml>
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337
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338 <xml name="gamma" token_default_value="1.0" token_label="Scaling parameter" token_help_text=" ">
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339 <param argument="gamma" type="float" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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340 </xml>
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341
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342 <xml name="degree" token_default_value="3" token_label="Degree of the polynomial" token_help_text=" ">
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343 <param argument="degree" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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344 </xml>
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345
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346 <xml name="coef0" token_default_value="1" token_label="Zero coefficient" token_help_text=" ">
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347 <param argument="coef0" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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348 </xml>
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349
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350 <xml name="pos_label" token_default_value="">
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351 <param argument="pos_label" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Label of the positive class" help=" "/>
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352 </xml>
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353
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354 <xml name="average">
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355 <param argument="average" type="select" optional="true" label="Averaging type" help=" ">
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356 <option value="micro">Calculate metrics globally by counting the total true positives, false negatives and false positives. (micro)</option>
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357 <option value="samples">Calculate metrics for each instance, and find their average. Only meaningful for multilabel. (samples)</option>
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358 <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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359 <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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360 <option value="None">None</option>
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361 <yield/>
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362 </param>
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363 </xml>
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364
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365 <xml name="beta">
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366 <param argument="beta" type="float" value="1.0" label="The strength of recall versus precision in the F-score" help=" "/>
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367 </xml>
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368
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369
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370 <!--Data interface-->
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371 <xml name="tabular_input">
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372 <param name="infile" type="data" format="tabular" label="Data file with numeric values"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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373 <param name="start_column" type="data_column" data_ref="infile" optional="True" label="Select a subset of data. Start column:" />
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374 <param name="end_column" type="data_column" data_ref="infile" optional="True" label="End column:" />
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375 </xml>
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376
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377 <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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378 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
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379 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/>
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380 <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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381 <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
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382 <yield/>
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383 </xml>
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384
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385 <xml name="samples_tabular" token_multiple1="False" token_multiple2="False">
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386 <param name="infile1" type="data" format="tabular" label="Training samples dataset:"/>
4
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387 <param name="header1" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
0
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388 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/>
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389 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels:"/>
4
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390 <param name="header2" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
0
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391 <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
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392 <yield/>
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393 </xml>
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394
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395 <xml name="clf_inputs_extended" token_label1=" " token_label2=" " token_multiple="False">
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396 <conditional name="true_columns">
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397 <param name="selected_input1" type="select" label="Select the input type of true labels dataset:">
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398 <option value="tabular" selected="true">Tabular</option>
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399 <option value="sparse">Sparse</option>
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400 </param>
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401 <when value="tabular">
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402 <param name="infile1" type="data" label="@LABEL1@"/>
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403 <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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404 </when>
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405 <when value="sparse">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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406 <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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407 </when>
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408 </conditional>
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409 <conditional name="predicted_columns">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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410 <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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411 <option value="tabular" selected="true">Tabular</option>
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412 <option value="sparse">Sparse</option>
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413 </param>
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414 <when value="tabular">
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415 <param name="infile2" type="data" label="@LABEL2@"/>
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416 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
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417 </when>
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418 <when value="sparse">
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419 <param name="infile2" type="data" format="txt" label="@LABEL1@"/>
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420 </when>
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421 </conditional>
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422 </xml>
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423
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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424 <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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425 <param name="infile1" type="data" format="tabular" label="@LABEL1@"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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426 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select the target column:"/>
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427 <param name="infile2" type="data" format="tabular" label="@LABEL2@"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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428 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
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429 </xml>
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430
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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431 <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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432 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):">
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433 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/>
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434 </repeat>
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435 </xml>
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436
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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437 <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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438 <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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439 <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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440 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
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441 </xml>
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442
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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443 <xml name="sl_mixed_input">
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diff changeset
444 <conditional name="input_options">
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445 <param name="selected_input" type="select" label="Select input type:">
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446 <option value="tabular" selected="true">tabular data</option>
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447 <option value="sparse">sparse matrix</option>
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448 </param>
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449 <when value="tabular">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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450 <expand macro="samples_tabular" multiple1="true"/>
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451 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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452 <when value="sparse">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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453 <expand macro="sparse_target"/>
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454 </when>
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455 </conditional>
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456 </xml>
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457
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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458 <xml name="multitype_input" token_format="tabular" token_help="All datasets with tabular format are supporetd.">
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diff changeset
459 <param name="infile_transform" type="data" format="@FORMAT@" label="Select a dataset to transform:" help="@HELP@"/>
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460 </xml>
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461
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462
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
463 <!--Advanced options-->
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464 <xml name="nn_advanced_options">
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465 <section name="options" title="Advanced Options" expanded="False">
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466 <yield/>
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467 <param argument="weights" type="select" label="Weight function" help="Used in prediction.">
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468 <option value="uniform" selected="true">Uniform weights. All points in each neighborhood are weighted equally. (Uniform)</option>
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469 <option value="distance">Weight points by the inverse of their distance. (Distance)</option>
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470 </param>
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471 <param argument="algorithm" type="select" label="Neighbor selection algorithm" help=" ">
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472 <option value="auto" selected="true">Auto</option>
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473 <option value="ball_tree">BallTree</option>
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474 <option value="kd_tree">KDTree</option>
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475 <option value="brute">Brute-force</option>
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476 </param>
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477 <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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478 <!--param name="metric"-->
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479 <!--param name="p"-->
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480 <!--param name="metric_params"-->
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481 </section>
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482 </xml>
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483
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484 <xml name="svc_advanced_options">
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485 <section name="options" title="Advanced Options" expanded="False">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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486 <yield/>
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487 <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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488 <option value="rbf" selected="true">rbf</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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489 <option value="linear">linear</option>
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490 <option value="poly">poly</option>
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491 <option value="sigmoid">sigmoid</option>
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492 <option value="precomputed">precomputed</option>
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493 </param>
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494 <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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495 <!--TODO: param argument="gamma" float, optional (default=’auto’) -->
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496 <param argument="coef0" type="float" optional="true" value="0.0" label="Zero coefficient (polynomial and sigmoid kernels only)"
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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497 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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498 <param argument="shrinking" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
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499 label="Use the shrinking heuristic" help=" "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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500 <param argument="probability" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false"
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501 label="Enable probability estimates. " help="This must be enabled prior to calling fit, and will slow down that method."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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502 <!-- param argument="cache_size"-->
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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503 <!--expand macro="class_weight"/-->
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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504 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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505 <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."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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506 <!--param argument="decision_function_shape"-->
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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507 <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."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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508 </section>
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509 </xml>
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510
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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511 <xml name="spectral_clustering_advanced_options">
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512 <section name="options" title="Advanced Options" expanded="False">
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diff changeset
513 <expand macro="n_clusters"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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514 <param argument="eigen_solver" type="select" value="" label="Eigen solver" help="The eigenvalue decomposition strategy to use.">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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515 <option value="arpack" selected="true">arpack</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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516 <option value="lobpcg">lobpcg</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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517 <option value="amg">amg</option>
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518 <!--None-->
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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519 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
520 <expand macro="random_state"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
521 <expand macro="n_init"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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522 <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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523 <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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524 <option value="rbf" selected="true">RBF</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
525 <option value="precomputed">precomputed</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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526 <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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527 </param>
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528 <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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529 <!--param argument="eigen_tol"-->
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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530 <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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diff changeset
531 <option value="kmeans" selected="true">kmeans</option>
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532 <option value="discretize">discretize</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
533 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
534 <param argument="degree" type="integer" optional="true" value="3"
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
535 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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diff changeset
536 <param argument="coef0" type="integer" optional="true" value="1"
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
537 label="Zero coefficient (polynomial and sigmoid kernels only)" help="Ignored by other kernels. dafault : 1 "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
538 <!--param argument="kernel_params"-->
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
539 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
540 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
541
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
542 <xml name="minibatch_kmeans_advanced_options">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
543 <section name="options" title="Advanced Options" expanded="False">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
544 <expand macro="n_clusters"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
545 <expand macro="init"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
546 <expand macro="n_init" default_value="3"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
547 <expand macro="max_iter" default_value="100"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
548 <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
bgruening
parents:
diff changeset
549 <expand macro="random_state"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
550 <param argument="batch_size" type="integer" optional="true" value="100" label="Batch size" help="Size of the mini batches."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
551 <!--param argument="compute_labels"-->
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
552 <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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diff changeset
553 Convergence detection based on inertia (the consecutive number of mini batches that doe not yield an improvement on the smoothed inertia).
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
554 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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diff changeset
555 <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
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diff changeset
556 <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
557 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
558 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
559
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
560 <xml name="kmeans_advanced_options">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
561 <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
562 <expand macro="n_clusters"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
563 <expand macro="init"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
564 <expand macro="n_init"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
565 <expand macro="max_iter"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
566 <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
567 <!--param argument="precompute_distances"/-->
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
568 <expand macro="random_state"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
569 <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."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
570 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
571 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
572
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
573 <xml name="birch_advanced_options">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
574 <section name="options" title="Advanced Options" expanded="False">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
575 <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
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diff changeset
576 <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
577 <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
578 <!--param argument="compute_labels"/-->
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
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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="dbscan_advanced_options">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
583 <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
584 <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
585 <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
586 <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
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diff changeset
587 <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
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diff changeset
588 <option value="auto" selected="true">auto</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
589 <option value="ball_tree">ball_tree</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
590 <option value="kd_tree">kd_tree</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
591 <option value="brute">brute</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
592 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
593 <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
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diff changeset
594 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
595 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
596
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
597 <xml name="clustering_algorithms_options">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
598 <conditional name="algorithm_options">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
599 <param name="selected_algorithm" type="select" label="Clustering Algorithm">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
600 <option value="KMeans" selected="true">KMeans</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
601 <option value="SpectralClustering">Spectral Clustering</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
602 <option value="MiniBatchKMeans">Mini Batch KMeans</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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603 <option value="DBSCAN">DBSCAN</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
604 <option value="Birch">Birch</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
605 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
606 <when value="KMeans">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
607 <expand macro="kmeans_advanced_options"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
608 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
609 <when value="DBSCAN">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
610 <expand macro="dbscan_advanced_options"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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611 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
612 <when value="Birch">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
613 <expand macro="birch_advanced_options"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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614 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
615 <when value="SpectralClustering">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
616 <expand macro="spectral_clustering_advanced_options"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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617 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
618 <when value="MiniBatchKMeans">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
619 <expand macro="minibatch_kmeans_advanced_options"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
620 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
621 </conditional>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
622 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
623
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
624 <xml name="distance_metrics">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
625 <param argument="metric" type="select" label="Distance metric" help=" ">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
626 <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
627 <option value="cityblock">cityblock</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
628 <option value="cosine">cosine</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
629 <option value="l1">l1</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
630 <option value="l2">l2</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
631 <option value="manhattan">manhattan</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
632 <yield/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
633 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
634 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
635
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
636 <xml name="distance_nonsparse_metrics">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
637 <option value="braycurtis">braycurtis</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
638 <option value="canberra">canberra</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
639 <option value="chebyshev">chebyshev</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
640 <option value="correlation">correlation</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
641 <option value="dice">dice</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
642 <option value="hamming">hamming</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
643 <option value="jaccard">jaccard</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
644 <option value="kulsinski">kulsinski</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
645 <option value="mahalanobis">mahalanobis</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
646 <option value="matching">matching</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
647 <option value="minkowski">minkowski</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
648 <option value="rogerstanimoto">rogerstanimoto</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
649 <option value="russellrao">russellrao</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
650 <option value="seuclidean">seuclidean</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
651 <option value="sokalmichener">sokalmichener</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
652 <option value="sokalsneath">sokalsneath</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
653 <option value="sqeuclidean">sqeuclidean</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
654 <option value="yule">yule</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
655 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
656
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
657 <xml name="pairwise_kernel_metrics">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
658 <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
659 <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
660 <option value="sigmoid">sigmoid</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
661 <option value="polynomial">polynomial</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
662 <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
663 <option value="chi2">chi2</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
664 <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
665 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
666 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
667
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
668 <xml name="sparse_pairwise_metric_functions">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
669 <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
670 <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
671 <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
672 <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
673 <yield/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
674 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
675 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
676
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
677 <xml name="pairwise_metric_functions">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
678 <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
679 <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
680 <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
681 <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
682 <option value="pairwise_kernels">Kernel</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
683 <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
684 <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
685 <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
686 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
687
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
688 <xml name="sparse_pairwise_condition">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
689 <when value="pairwise_distances">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
690 <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
691 <expand macro="distance_metrics">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
692 <yield/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
693 </expand>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
694 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
695 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
696 <when value="euclidean_distances">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
697 <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
698 <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
699 label="Return squared Euclidean distances" help=" "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
700 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
701 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
702 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
703
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
704 <xml name="argmin_distance_condition">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
705 <when value="pairwise_distances_argmin">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
706 <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
707 <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
708 <expand macro="distance_metrics">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
709 <yield/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
710 </expand>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
711 <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
712 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
713 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
714 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
715
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
716 <xml name="sparse_preprocessors">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
717 <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
718 <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
719 <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
720 <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
721 <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
722 <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
723 <yield/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
724 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
725 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
726
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
727 <xml name="sparse_preprocessor_options">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
728 <when value="Binarizer">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
729 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
730 <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
731 <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
732 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
733 <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
734 label="Threshold"
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
735 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
736 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
737 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
738 <when value="Imputer">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
739 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
740 <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
741 <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
742 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
743 <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
744 <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
745 <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
746 <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
747 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
748 <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
749 label="Placeholder for missing values" help="For missing values encoded as numpy.nan, use the string value “NaN”"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
750 <param argument="axis" type="boolean" optional="true" truevalue="1" falsevalue="0"
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
751 label="Impute along axis = 1" help="If fasle, axis = 0 is selected for imputation. "/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
752 <!--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
753 <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
754 <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
755 </param-->
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
756 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
757 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
758 <when value="StandardScaler">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
759 <expand macro="multitype_input"/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
760 <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
761 <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
762 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
763 <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
764 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
765 <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
766 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
767 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
768 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
769 <when value="MaxAbsScaler">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
770 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
771 <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
772 <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
773 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
774 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
775 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
776 <when value="Normalizer">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
777 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
778 <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
779 <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
780 <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
781 <option value="l2">l2</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
782 <option value="max">max</option>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
783 </param>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
784 <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
785 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
786 </section>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
787 </when>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
788 <yield/>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
789 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
790
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
791 <!-- Outputs -->
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
792
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
793 <xml name="output">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
794 <outputs>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
795 <data format="tabular" name="outfile_predict">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
796 <filter>selected_tasks['selected_task'] == 'load'</filter>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
797 </data>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
798 <data format="zip" name="outfile_fit">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
799 <filter>selected_tasks['selected_task'] == 'train'</filter>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
800 </data>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
801 </outputs>
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802 </xml>
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parents:
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803
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
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804
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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805 <!--Citations-->
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806 <xml name="eden_citation">
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807 <citations>
3
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parents: 2
diff changeset
808 <citation type="doi">10.5281/zenodo.15094</citation>
0
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809 </citations>
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810 </xml>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
811
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
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812 <xml name="sklearn_citation">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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813 <citations>
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
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814 <citation type="bibtex">
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parents:
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815 @article{scikit-learn,
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816 title={Scikit-learn: Machine Learning in {P}ython},
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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817 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
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818 and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
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819 and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
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820 Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
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parents:
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821 journal={Journal of Machine Learning Research},
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parents:
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822 volume={12},
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parents:
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823 pages={2825--2830},
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parents:
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824 year={2011}
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825 url = {https://github.com/scikit-learn/scikit-learn}
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parents:
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826 }
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827 </citation>
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828 </citations>
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parents:
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829 </xml>
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parents:
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830
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
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831 <xml name="scipy_citation">
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parents:
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832 <citations>
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parents:
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833 <citation type="bibtex">
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
834 @Misc{,
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
835 author = {Eric Jones and Travis Oliphant and Pearu Peterson and others},
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
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836 title = {{SciPy}: Open source scientific tools for {Python}},
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
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837 year = {2001--},
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
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838 url = "http://www.scipy.org/",
e0067d9baffc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
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839 note = {[Online; accessed 2016-04-09]}
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parents:
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840 }
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parents:
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841 </citation>
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parents:
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842 </citations>
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parents:
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843 </xml>
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parents:
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844
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845 </macros>