Mercurial > repos > bgruening > sklearn_sample_generator

annotate main_macros.xml @ 7:cd93ef24abb7 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76
author bgruening
date Tue, 13 Mar 2018 04:50:22 -0400
parents 7d15131814a5
children 956bb8dcde71
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f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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1 <macros>
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2 <token name="@VERSION@">0.9</token>
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3
4
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4 <token name="@COLUMNS_FUNCTION@">
7
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5 def read_columns(f, c, **args):
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6 data = pandas.read_csv(f, **args)
4
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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
0
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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>
0
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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>
3
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25 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
0
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26 </stdio>
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27 </xml>
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28
2
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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">
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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>
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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."/>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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40 <conditional name="prediction_options">
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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>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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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>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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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">
3
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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
2
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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">
3
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67 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/>
2
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68 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
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69 <conditional name="prediction_options">
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70 <param name="prediction_option" type="select" label="Select the type of prediction">
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71 <option value="predict">Predict class labels</option>
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72 <option value="advanced">Include advanced options</option>
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73 </param>
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74 <when value="predict">
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75 </when>
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76 <when value="advanced">
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77 </when>
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78 </conditional>
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79 </when>
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80 <when value="train">
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81 <conditional name="selected_algorithms">
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82 <yield />
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83 </conditional>
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84 </when>
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85 </conditional>
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86 </xml>
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87
0
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88 <xml name="advanced_section">
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89 <section name="options" title="Advanced Options" expanded="False">
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90 <yield />
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91 </section>
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92 </xml>
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93
2
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94
5
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95 <!--Generalized Linear Models-->
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96 <xml name="loss" token_help=" " token_select="false">
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97 <param argument="loss" type="select" label="Loss function" help="@HELP@">
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98 <option value="squared_loss" selected="@SELECT@">squared loss</option>
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99 <option value="huber">huber</option>
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100 <option value="epsilon_insensitive">epsilon insensitive</option>
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101 <option value="squared_epsilon_insensitive">squared epsilon insensitive</option>
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102 <yield/>
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103 </param>
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104 </xml>
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105
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106 <xml name="penalty" token_help=" ">
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107 <param argument="penalty" type="select" label="Penalty (regularization term)" help="@HELP@">
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108 <option value="l2" selected="true">l2</option>
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109 <option value="l1">l1</option>
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110 <option value="elasticnet">elastic net</option>
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111 <option value="none">none</option>
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112 <yield/>
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113 </param>
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114 </xml>
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115
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116 <xml name="l1_ratio" token_default_value="0.15" token_help=" ">
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117 <param argument="l1_ratio" type="float" value="@DEFAULT_VALUE@" label="Elastic Net mixing parameter" help="@HELP@"/>
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118 </xml>
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119
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120 <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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121 <param argument="epsilon" type="float" value="@DEFAULT_VALUE@" label="Epsilon (epsilon-sensitive loss functions only)" help="@HELP@"/>
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122 </xml>
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123
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124 <xml name="learning_rate_s" token_help=" " token_selected1="false" token_selected2="false">
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125 <param argument="learning_rate" type="select" optional="true" label="Learning rate schedule" help="@HELP@">
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126 <option value="optimal" selected="@SELECTED1@">optimal</option>
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127 <option value="constant">constant</option>
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128 <option value="invscaling" selected="@SELECTED2@">inverse scaling</option>
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129 <yield/>
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130 </param>
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131 </xml>
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132
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133 <xml name="eta0" token_default_value="0.0" token_help="Used with ‘constant’ or ‘invscaling’ schedules. ">
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134 <param argument="eta0" type="float" value="@DEFAULT_VALUE@" label="Initial learning rate" help="@HELP@"/>
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135 </xml>
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136
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137 <xml name="power_t" token_default_value="0.5" token_help=" ">
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138 <param argument="power_t" type="float" value="@DEFAULT_VALUE@" label="Exponent for inverse scaling learning rate" help="@HELP@"/>
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139 </xml>
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140
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141 <xml name="normalize" token_checked="false" token_help=" ">
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142 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Normalize samples before training" help=" "/>
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143 </xml>
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144
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145 <xml name="copy_X" token_checked="true" token_help=" ">
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146 <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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147 </xml>
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148
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149 <xml name="ridge_params">
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150 <expand macro="normalize"/>
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151 <expand macro="alpha" default_value="1.0"/>
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152 <expand macro="fit_intercept"/>
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153 <expand macro="max_iter" default_value=""/>
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154 <expand macro="tol" default_value="0.001" help_text="Precision of the solution. "/>
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155 <!--class_weight-->
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156 <expand macro="copy_X"/>
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157 <param argument="solver" type="select" value="" label="Solver to use in the computational routines" help=" ">
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158 <option value="auto" selected="true">auto</option>
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159 <option value="svd">svd</option>
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160 <option value="cholesky">cholesky</option>
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161 <option value="lsqr">lsqr</option>
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162 <option value="sparse_cg">sparse_cg</option>
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163 <option value="sag">sag</option>
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164 </param>
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165 <expand macro="random_state"/>
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166 </xml>
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167
2
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168 <!--Ensemble methods-->
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169 <xml name="n_estimators" token_default_value="10" token_help=" ">
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170 <param argument="n_estimators" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of trees in the forest" help="@HELP@"/>
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171 </xml>
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172
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173 <xml name="max_depth" token_default_value="" token_help=" ">
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174 <param argument="max_depth" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@"/>
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175 </xml>
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176
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177 <xml name="min_samples_split" token_default_value="2" token_help=" ">
6
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178 <param argument="min_samples_split" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Minimum number of samples required to split an internal node" help="@HELP@"/>
2
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179 </xml>
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180
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181 <xml name="min_samples_leaf" token_default_value="1" token_help=" ">
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182 <param argument="min_samples_leaf" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Minimum number of samples in newly created leaves" help="@HELP@"/>
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183 </xml>
5
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184
2
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185 <xml name="min_weight_fraction_leaf" token_default_value="0.0" token_help=" ">
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186 <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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187 </xml>
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188
2
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189 <xml name="max_leaf_nodes" token_default_value="" token_help=" ">
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190 <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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191 </xml>
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192
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193 <xml name="bootstrap" token_checked="true" token_help=" ">
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194 <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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195 </xml>
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196
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197 <xml name="criterion" token_help=" ">
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198 <param argument="criterion" type="select" label="Function to measure the quality of a split" help=" ">
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199 <option value="gini" selected="true">Gini impurity</option>
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200 <option value="entropy">Information gain</option>
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201 <yield/>
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202 </param>
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203 </xml>
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204
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205 <xml name="oob_score" token_checked="false" token_help=" ">
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206 <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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207 </xml>
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208
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209 <xml name="max_features" token_default_value="auto" token_help="This could be an integer, float, string, or None. For more information please refer to help. ">
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210 <param argument="max_features" type="text" optional="true" value="@DEFAULT_VALUE@" label="Number of features for finding the best split" help="@HELP@"/>
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211 </xml>
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212
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213 <xml name="learning_rate" token_default_value="1.0" token_help=" ">
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214 <param argument="learning_rate" type="float" optional="true" value="@DEFAULT_VALUE@" label="Learning rate" help="@HELP@"/>
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215 </xml>
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216
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217
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218 <!--Parameters-->
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219 <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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220 <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@"/>
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221 </xml>
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222
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223 <xml name="n_clusters" token_default_value="8">
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224 <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" "/>
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225 </xml>
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226
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227 <xml name="fit_intercept" token_checked="true">
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228 <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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229 </xml>
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230
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231 <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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232 <param argument="n_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@"/>
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233 </xml>
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234
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235 <xml name="shuffle" token_checked="true" token_help_text=" " token_label="Shuffle data after each iteration">
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236 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="@LABEL@" help="@HELP_TEXT@"/>
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237 </xml>
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238
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239 <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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240 <param argument="random_state" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Random seed number" help="@HELP_TEXT@"/>
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241 </xml>
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242
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243 <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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244 <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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245 </xml>
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246
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247 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term.">
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248 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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249 </xml>
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250
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251 <!--xml name="class_weight" token_default_value="" token_help_text="">
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252 <param argument="class_weight" type="" optional="true" value="@DEFAULT_VALUE@" label="" help="@HELP_TEXT@"/>
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253 </xml-->
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254
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255 <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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256 <param argument="alpha" type="float" optional="true" value="@DEFAULT_VALUE@" label="Regularization coefficient" help="@HELP_TEXT@"/>
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257 </xml>
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258
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259 <xml name="n_samples" token_default_value="100" token_help_text="The total number of points equally divided among clusters.">
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260 <param argument="n_samples" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of samples" help="@HELP_TEXT@"/>
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261 </xml>
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262
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263 <xml name="n_features" token_default_value="2" token_help_text="Number of different numerical properties produced for each sample.">
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264 <param argument="n_features" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of features" help="@HELP_TEXT@"/>
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265 </xml>
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266
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267 <xml name="noise" token_default_value="0.0" token_help_text="Floating point number. ">
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268 <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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269 </xml>
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270
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271 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term. ">
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272 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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273 </xml>
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274
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275 <xml name="max_iter" token_default_value="300" token_label="Maximum number of iterations per single run" token_help_text=" ">
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276 <param argument="max_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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277 </xml>
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278
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279 <xml name="n_init" token_default_value="10" >
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280 <param argument="n_init" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of runs with different centroid seeds" help=" "/>
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281 </xml>
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282
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283 <xml name="init">
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284 <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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285 <option value="k-means++">k-means++</option>
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286 <option value="random">random</option>
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287 </param>
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288 </xml>
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289
1
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290 <xml name="gamma" token_default_value="1.0" token_label="Scaling parameter" token_help_text=" ">
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291 <param argument="gamma" type="float" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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292 </xml>
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293
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294 <xml name="degree" token_default_value="3" token_label="Degree of the polynomial" token_help_text=" ">
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295 <param argument="degree" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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296 </xml>
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297
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298 <xml name="coef0" token_default_value="1" token_label="Zero coefficient" token_help_text=" ">
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299 <param argument="coef0" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
2
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300 </xml>
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301
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302 <xml name="pos_label" token_default_value="">
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303 <param argument="pos_label" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Label of the positive class" help=" "/>
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304 </xml>
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305
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306 <xml name="average">
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307 <param argument="average" type="select" optional="true" label="Averaging type" help=" ">
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308 <option value="micro">Calculate metrics globally by counting the total true positives, false negatives and false positives. (micro)</option>
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309 <option value="samples">Calculate metrics for each instance, and find their average. Only meaningful for multilabel. (samples)</option>
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310 <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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311 <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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312 <option value="None">None</option>
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313 <yield/>
2
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314 </param>
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315 </xml>
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316
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317 <xml name="beta">
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318 <param argument="beta" type="float" value="1.0" label="The strength of recall versus precision in the F-score" help=" "/>
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319 </xml>
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320
5
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321
2
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322 <!--Data interface-->
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323 <xml name="tabular_input">
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324 <param name="infile" type="data" format="tabular" label="Data file with numeric values"/>
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325 <param name="start_column" type="data_column" data_ref="infile" optional="True" label="Select a subset of data. Start column:" />
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326 <param name="end_column" type="data_column" data_ref="infile" optional="True" label="End column:" />
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327 </xml>
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328
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329 <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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330 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
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331 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/>
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332 <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/>
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333 <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
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334 <yield/>
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335 </xml>
1
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336
5
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337 <xml name="samples_tabular" token_multiple1="False" token_multiple2="False">
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338 <param name="infile1" type="data" format="tabular" label="Training samples dataset:"/>
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339 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/>
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340 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels:"/>
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341 <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
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342 <yield/>
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343 </xml>
4
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344
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345 <xml name="clf_inputs_extended" token_label1=" " token_label2=" " token_multiple="False">
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346 <conditional name="true_columns">
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347 <param name="selected_input1" type="select" label="Select the input type of true labels dataset:">
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348 <option value="tabular" selected="true">Tabular</option>
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349 <option value="sparse">Sparse</option>
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350 </param>
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351 <when value="tabular">
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352 <param name="infile1" type="data" label="@LABEL1@"/>
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353 <param name="col1" type="data_column" data_ref="infile1" label="Select the target column:"/>
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354 </when>
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355 <when value="sparse">
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356 <param name="infile1" type="data" format="txt" label="@LABEL1@"/>
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357 </when>
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358 </conditional>
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359 <conditional name="predicted_columns">
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360 <param name="selected_input2" type="select" label="Select the input type of predicted labels dataset:">
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361 <option value="tabular" selected="true">Tabular</option>
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362 <option value="sparse">Sparse</option>
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363 </param>
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364 <when value="tabular">
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365 <param name="infile2" type="data" label="@LABEL2@"/>
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366 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
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367 </when>
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368 <when value="sparse">
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369 <param name="infile2" type="data" format="txt" label="@LABEL1@"/>
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370 </when>
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371 </conditional>
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372 </xml>
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373
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374 <xml name="clf_inputs" token_label1="Dataset containing true labels (tabular):" token_label2="Dataset containing predicted values (tabular):" token_multiple1="False" token_multiple="False">
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375 <param name="infile1" type="data" format="tabular" label="@LABEL1@"/>
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376 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select the target column:"/>
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377 <param name="infile2" type="data" format="tabular" label="@LABEL2@"/>
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378 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
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379 </xml>
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380
1
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381 <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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382 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):">
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383 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/>
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384 </repeat>
5
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385 </xml>
0
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386
2
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387 <xml name="sparse_target" token_label1="Select a sparse matrix:" token_label2="Select the tabular containing true labels:" token_multiple="False" token_format1="txt" token_format2="tabular" token_help1="" token_help2="">
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388 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
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389 <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/>
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390 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
0
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391 </xml>
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392
2
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393 <xml name="sl_mixed_input">
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394 <conditional name="input_options">
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395 <param name="selected_input" type="select" label="Select input type:">
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396 <option value="tabular" selected="true">tabular data</option>
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397 <option value="sparse">sparse matrix</option>
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398 </param>
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399 <when value="tabular">
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400 <expand macro="samples_tabular" multiple1="true"/>
2
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401 </when>
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402 <when value="sparse">
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403 <expand macro="sparse_target"/>
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404 </when>
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405 </conditional>
0
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406 </xml>
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407
3
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408 <xml name="multitype_input" token_format="tabular" token_help="All datasets with tabular format are supporetd.">
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409 <param name="infile_transform" type="data" format="@FORMAT@" label="Select a dataset to transform:" help="@HELP@"/>
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410 </xml>
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411
0
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412
2
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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413 <!--Advanced options-->
0
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414 <xml name="nn_advanced_options">
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415 <section name="options" title="Advanced Options" expanded="False">
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416 <yield/>
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417 <param argument="weights" type="select" label="Weight function" help="Used in prediction.">
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418 <option value="uniform" selected="true">Uniform weights. All points in each neighborhood are weighted equally. (Uniform)</option>
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419 <option value="distance">Weight points by the inverse of their distance. (Distance)</option>
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420 </param>
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421 <param argument="algorithm" type="select" label="Neighbor selection algorithm" help=" ">
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422 <option value="auto" selected="true">Auto</option>
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423 <option value="ball_tree">BallTree</option>
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424 <option value="kd_tree">KDTree</option>
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425 <option value="brute">Brute-force</option>
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426 </param>
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427 <param argument="leaf_size" type="integer" value="30" label="Leaf size" help="Used with BallTree and KDTree. Affects the time and memory usage of the constructed tree."/>
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428 <!--param name="metric"-->
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429 <!--param name="p"-->
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430 <!--param name="metric_params"-->
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431 </section>
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432 </xml>
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433
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434 <xml name="svc_advanced_options">
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435 <section name="options" title="Advanced Options" expanded="False">
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436 <yield/>
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437 <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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438 <option value="rbf" selected="true">rbf</option>
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439 <option value="linear">linear</option>
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440 <option value="poly">poly</option>
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441 <option value="sigmoid">sigmoid</option>
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442 <option value="precomputed">precomputed</option>
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443 </param>
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444 <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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445 <!--TODO: param argument="gamma" float, optional (default=’auto’) -->
5
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446 <param argument="coef0" type="float" optional="true" value="0.0" label="Zero coefficient (polynomial and sigmoid kernels only)"
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447 help="Independent term in kernel function. dafault: 0.0 "/>
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448 <param argument="shrinking" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
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449 label="Use the shrinking heuristic" help=" "/>
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450 <param argument="probability" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false"
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451 label="Enable probability estimates. " help="This must be enabled prior to calling fit, and will slow down that method."/>
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452 <!-- param argument="cache_size"-->
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453 <!--expand macro="class_weight"/-->
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454 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. "/>
0
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455 <expand macro="max_iter" default_value="-1" label="Solver maximum number of iterations" help_text="Hard limit on iterations within solver, or -1 for no limit."/>
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456 <!--param argument="decision_function_shape"-->
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457 <expand macro="random_state" help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data for probability estimation. A fixed seed allows reproducible results."/>
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458 </section>
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459 </xml>
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460
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461 <xml name="spectral_clustering_advanced_options">
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462 <section name="options" title="Advanced Options" expanded="False">
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463 <expand macro="n_clusters"/>
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464 <param argument="eigen_solver" type="select" value="" label="Eigen solver" help="The eigenvalue decomposition strategy to use.">
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465 <option value="arpack" selected="true">arpack</option>
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466 <option value="lobpcg">lobpcg</option>
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467 <option value="amg">amg</option>
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468 <!--None-->
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469 </param>
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470 <expand macro="random_state"/>
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471 <expand macro="n_init"/>
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472 <param argument="gamma" type="float" optional="true" value="1.0" label="Kernel scaling factor" help="Scaling factor of RBF, polynomial, exponential chi^2 and sigmoid affinity kernel. Ignored for affinity=''nearest_neighbors''."/>
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473 <param argument="affinity" type="select" label="Affinity" help="Affinity kernel to use. ">
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474 <option value="rbf" selected="true">RBF</option>
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475 <option value="precomputed">precomputed</option>
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476 <option value="nearest_neighbors">Nearset neighbors</option>
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477 </param>
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478 <param argument="n_neighbors" type="integer" optional="true" value="10" label="Number of neighbors" help="Number of neighbors to use when constructing the affinity matrix using the nearest neighbors method. Ignored for affinity=''rbf''"/>
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479 <!--param argument="eigen_tol"-->
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480 <param argument="assign_labels" type="select" label="Assign labels" help="The strategy to use to assign labels in the embedding space.">
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481 <option value="kmeans" selected="true">kmeans</option>
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482 <option value="discretize">discretize</option>
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483 </param>
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484 <param argument="degree" type="integer" optional="true" value="3"
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485 label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/>
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486 <param argument="coef0" type="integer" optional="true" value="1"
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487 label="Zero coefficient (polynomial and sigmoid kernels only)" help="Ignored by other kernels. dafault : 1 "/>
0
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488 <!--param argument="kernel_params"-->
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489 </section>
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490 </xml>
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491
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492 <xml name="minibatch_kmeans_advanced_options">
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493 <section name="options" title="Advanced Options" expanded="False">
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494 <expand macro="n_clusters"/>
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495 <expand macro="init"/>
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496 <expand macro="n_init" default_value="3"/>
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497 <expand macro="max_iter" default_value="100"/>
5
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498 <expand macro="tol" help_text="Early stopping heuristics based on normalized center change. To disable set to 0.0 ."/>
0
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499 <expand macro="random_state"/>
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500 <param argument="batch_size" type="integer" optional="true" value="100" label="Batch size" help="Size of the mini batches."/>
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501 <!--param argument="compute_labels"-->
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502 <param argument="max_no_improvement" type="integer" optional="true" value="10" label="Maximum number of improvement attempts" help="
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503 Convergence detection based on inertia (the consecutive number of mini batches that doe not yield an improvement on the smoothed inertia).
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504 To disable, set max_no_improvement to None. "/>
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505 <param argument="init_size" type="integer" optional="true" value="" label="Number of random initialization samples" help="Number of samples to randomly sample for speeding up the initialization . ( default: 3 * batch_size )"/>
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506 <param argument="reassignment_ratio" type="float" optional="true" value="0.01" label="Re-assignment ratio" help="Controls the fraction of the maximum number of counts for a center to be reassigned. Higher values yield better clustering results."/>
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507 </section>
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508 </xml>
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509
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510 <xml name="kmeans_advanced_options">
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511 <section name="options" title="Advanced Options" expanded="False">
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512 <expand macro="n_clusters"/>
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513 <expand macro="init"/>
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514 <expand macro="n_init"/>
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515 <expand macro="max_iter"/>
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516 <expand macro="tol" default_value="0.0001" help_text="Relative tolerance with regards to inertia to declare convergence."/>
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517 <!--param argument="precompute_distances"/-->
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518 <expand macro="random_state"/>
5
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519 <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."/>
0
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520 </section>
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521 </xml>
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522
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523 <xml name="birch_advanced_options">
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524 <section name="options" title="Advanced Options" expanded="False">
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525 <param argument="threshold" type="float" optional="true" value="0.5" label="Subcluster radius threshold" help="The radius of the subcluster obtained by merging a new sample; the closest subcluster should be less than the threshold to avoid a new subcluster."/>
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526 <param argument="branching_factor" type="integer" optional="true" value="50" label="Maximum number of subclusters per branch" help="Maximum number of CF subclusters in each node."/>
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527 <expand macro="n_clusters" default_value="3"/>
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528 <!--param argument="compute_labels"/-->
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529 </section>
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530 </xml>
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531
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532 <xml name="dbscan_advanced_options">
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533 <section name="options" title="Advanced Options" expanded="False">
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534 <param argument="eps" type="float" optional="true" value="0.5" label="Maximum neighborhood distance" help="The maximum distance between two samples for them to be considered as in the same neighborhood."/>
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535 <param argument="min_samples" type="integer" optional="true" value="5" label="Minimal core point density" help="The number of samples (or total weight) in a neighborhood for a point (including the point itself) to be considered as a core point."/>
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diff changeset
536 <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."/>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
537 <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.">
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
538 <option value="auto" selected="true">auto</option>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
539 <option value="ball_tree">ball_tree</option>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
540 <option value="kd_tree">kd_tree</option>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
541 <option value="brute">brute</option>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
542 </param>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
543 <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."/>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
544 </section>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
545 </xml>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
546
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
547 <xml name="clustering_algorithms_options">
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
548 <conditional name="algorithm_options">
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
549 <param name="selected_algorithm" type="select" label="Clustering Algorithm">
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
550 <option value="KMeans" selected="true">KMeans</option>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
551 <option value="SpectralClustering">Spectral Clustering</option>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
552 <option value="MiniBatchKMeans">Mini Batch KMeans</option>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
553 <option value="DBSCAN">DBSCAN</option>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
554 <option value="Birch">Birch</option>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
555 </param>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
556 <when value="KMeans">
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
557 <expand macro="kmeans_advanced_options"/>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
558 </when>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
559 <when value="DBSCAN">
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
560 <expand macro="dbscan_advanced_options"/>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
561 </when>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
562 <when value="Birch">
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
563 <expand macro="birch_advanced_options"/>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
564 </when>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
565 <when value="SpectralClustering">
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
566 <expand macro="spectral_clustering_advanced_options"/>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
567 </when>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
568 <when value="MiniBatchKMeans">
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
569 <expand macro="minibatch_kmeans_advanced_options"/>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
570 </when>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
571 </conditional>
f58c35905608 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
bgruening
parents:
diff changeset
572 </xml>
1
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
573
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
574 <xml name="distance_metrics">
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
575 <param argument="metric" type="select" label="Distance metric" help=" ">
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
576 <option value="euclidean" selected="true">euclidean</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
577 <option value="cityblock">cityblock</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
578 <option value="cosine">cosine</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
579 <option value="l1">l1</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
580 <option value="l2">l2</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
581 <option value="manhattan">manhattan</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
582 <yield/>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
583 </param>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
584 </xml>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
585
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
586 <xml name="distance_nonsparse_metrics">
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
587 <option value="braycurtis">braycurtis</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
588 <option value="canberra">canberra</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
589 <option value="chebyshev">chebyshev</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
590 <option value="correlation">correlation</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
591 <option value="dice">dice</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
592 <option value="hamming">hamming</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
593 <option value="jaccard">jaccard</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
594 <option value="kulsinski">kulsinski</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
595 <option value="mahalanobis">mahalanobis</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
596 <option value="matching">matching</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
597 <option value="minkowski">minkowski</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
598 <option value="rogerstanimoto">rogerstanimoto</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
599 <option value="russellrao">russellrao</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
600 <option value="seuclidean">seuclidean</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
601 <option value="sokalmichener">sokalmichener</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
602 <option value="sokalsneath">sokalsneath</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
603 <option value="sqeuclidean">sqeuclidean</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
604 <option value="yule">yule</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
605 </xml>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
606
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
607 <xml name="pairwise_kernel_metrics">
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
608 <param argument="metric" type="select" label="Pirwise Kernel metric" help=" ">
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
609 <option value="rbf" selected="true">rbf</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
610 <option value="sigmoid">sigmoid</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
611 <option value="polynomial">polynomial</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
612 <option value="linear" selected="true">linear</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
613 <option value="chi2">chi2</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
614 <option value="additive_chi2">additive_chi2</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
615 </param>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
616 </xml>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
617
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
618 <xml name="sparse_pairwise_metric_functions">
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
619 <param name="selected_metric_function" type="select" label="Select the pairwise metric you want to compute:">
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
620 <option value="euclidean_distances" selected="true">Euclidean distance matrix</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
621 <option value="pairwise_distances">Distance matrix</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
622 <option value="pairwise_distances_argmin">Minimum distances between one point and a set of points</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
623 <yield/>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
624 </param>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
625 </xml>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
626
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
627 <xml name="pairwise_metric_functions">
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
628 <option value="additive_chi2_kernel" >Additive chi-squared kernel</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
629 <option value="chi2_kernel">Exponential chi-squared kernel</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
630 <option value="linear_kernel">Linear kernel</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
631 <option value="manhattan_distances">L1 distances</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
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632 <option value="pairwise_kernels">Kernel</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
633 <option value="polynomial_kernel">Polynomial kernel</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
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634 <option value="rbf_kernel">Gaussian (rbf) kernel</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
635 <option value="laplacian_kernel">Laplacian kernel</option>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
636 </xml>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
637
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
638 <xml name="sparse_pairwise_condition">
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
639 <when value="pairwise_distances">
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
640 <section name="options" title="Advanced Options" expanded="False">
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
641 <expand macro="distance_metrics">
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
642 <yield/>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
643 </expand>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
644 </section>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
645 </when>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
646 <when value="euclidean_distances">
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
647 <section name="options" title="Advanced Options" expanded="False">
5
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
648 <param argument="squared" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false"
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
649 label="Return squared Euclidean distances" help=" "/>
1
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
650 </section>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
651 </when>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
652 </xml>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
653
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
654 <xml name="argmin_distance_condition">
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
655 <when value="pairwise_distances_argmin">
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
656 <section name="options" title="Advanced Options" expanded="False">
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
657 <param argument="axis" type="integer" optional="true" value="1" label="Axis" help="Axis along which the argmin and distances are to be computed."/>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
658 <expand macro="distance_metrics">
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
659 <yield/>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
660 </expand>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
661 <param argument="batch_size" type="integer" optional="true" value="500" label="Batch size" help="Number of rows to be processed in each batch run."/>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
662 </section>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
663 </when>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
664 </xml>
e61a463751e6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
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665
2
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
666 <xml name="sparse_preprocessors">
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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667 <param name="selected_pre_processor" type="select" label="Select a preprocessor:">
3
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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668 <option value="StandardScaler" selected="true">Standard Scaler (Standardizes features by removing the mean and scaling to unit variance)</option>
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
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669 <option value="Binarizer">Binarizer (Binarizes data)</option>
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
670 <option value="Imputer">Imputer (Completes missing values)</option>
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
671 <option value="MaxAbsScaler">Max Abs Scaler (Scales features by their maximum absolute value)</option>
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
672 <option value="Normalizer">Normalizer (Normalizes samples individually to unit norm)</option>
2
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
673 <yield/>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
674 </param>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
675 </xml>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
676
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
677 <xml name="sparse_preprocessor_options">
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
678 <when value="Binarizer">
3
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
679 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
2
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
680 <section name="options" title="Advanced Options" expanded="False">
5
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
681 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
682 label="Use a copy of data for precomputing binarization" help=" "/>
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
683 <param argument="threshold" type="float" optional="true" value="0.0"
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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684 label="Threshold"
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
685 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. "/>
2
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
686 </section>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
687 </when>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
688 <when value="Imputer">
3
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
689 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
690 <section name="options" title="Advanced Options" expanded="False">
5
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
691 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
692 label="Use a copy of data for precomputing imputation" help=" "/>
3
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
693 <param argument="strategy" type="select" optional="true" label="Imputation strategy" help=" ">
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
694 <option value="mean" selected="true">Replace missing values using the mean along the axis</option>
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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695 <option value="median">Replace missing values using the median along the axis</option>
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
696 <option value="most_frequent">Replace missing using the most frequent value along the axis</option>
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
697 </param>
5
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
698 <param argument="missing_values" type="text" optional="true" value="NaN"
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
699 label="Placeholder for missing values" help="For missing values encoded as numpy.nan, use the string value “NaN”"/>
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
700 <param argument="axis" type="boolean" optional="true" truevalue="1" falsevalue="0"
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
701 label="Impute along axis = 1" help="If fasle, axis = 0 is selected for imputation. "/>
3
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
702 <!--param argument="axis" type="select" optional="true" label="The axis along which to impute" help=" ">
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
703 <option value="0" selected="true">Impute along columns</option>
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
704 <option value="1">Impute along rows</option>
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
705 </param-->
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
706 </section>
2
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
707 </when>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
708 <when value="StandardScaler">
3
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
709 <expand macro="multitype_input"/>
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
710 <section name="options" title="Advanced Options" expanded="False">
5
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
711 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
712 label="Use a copy of data for performing inplace scaling" help=" "/>
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
713 <param argument="with_mean" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
714 label="Center the data before scaling" help=" "/>
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
715 <param argument="with_std" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
716 label="Scale the data to unit variance (or unit standard deviation)" help=" "/>
3
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
717 </section>
2
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
718 </when>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
719 <when value="MaxAbsScaler">
3
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
720 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
721 <section name="options" title="Advanced Options" expanded="False">
5
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
722 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
723 label="Use a copy of data for precomputing scaling" help=" "/>
3
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
724 </section>
2
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
725 </when>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
726 <when value="Normalizer">
3
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
727 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
728 <section name="options" title="Advanced Options" expanded="False">
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
729 <param argument="norm" type="select" optional="true" label="The norm to use to normalize non zero samples" help=" ">
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
730 <option value="l1" selected="true">l1</option>
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
731 <option value="l2">l2</option>
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
732 <option value="max">max</option>
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
733 </param>
5
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
734 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
735 label="Use a copy of data for precomputing row normalization" help=" "/>
3
ed56e50ebba9 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
736 </section>
2
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
737 </when>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
738 <yield/>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
739 </xml>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
740
5
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
741 <!-- Outputs -->
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
742
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
743 <xml name="output">
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
744 <outputs>
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
745 <data format="tabular" name="outfile_predict">
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
746 <filter>selected_tasks['selected_task'] == 'load'</filter>
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
747 </data>
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 4
diff changeset
748 <data format="zip" name="outfile_fit">
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
749 <filter>selected_tasks['selected_task'] == 'train'</filter>
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
750 </data>
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
751 </outputs>
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
752 </xml>
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents: 4
diff changeset
753
2
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
754
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
755 <!--Citations-->
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
756 <xml name="eden_citation">
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
757 <citations>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
758 <citation type="bibtex">
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
759 @misc{fabrizio_costa_2015_15094,
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
760 author = {Fabrizio Costa and
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
761 Björn Grüning and
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
762 gigolo},
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
763 title = {EDeN: EDeN - Graph Vectorizer},
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
764 month = feb,
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
765 year = 2015,
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
766 doi = {10.5281/zenodo.15094},
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
767 url = {http://dx.doi.org/10.5281/zenodo.15094}
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
768 }
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
769 }
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
770 </citation>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
771 </citations>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
772 </xml>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
773
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
774 <xml name="sklearn_citation">
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
775 <citations>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
776 <citation type="bibtex">
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
777 @article{scikit-learn,
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
778 title={Scikit-learn: Machine Learning in {P}ython},
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
779 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
780 and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
781 and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
782 Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
783 journal={Journal of Machine Learning Research},
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
784 volume={12},
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
785 pages={2825--2830},
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
786 year={2011}
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
787 url = {https://github.com/scikit-learn/scikit-learn}
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
788 }
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
789 </citation>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
790 </citations>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
791 </xml>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
792
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
793 <xml name="scipy_citation">
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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794 <citations>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
795 <citation type="bibtex">
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
796 @Misc{,
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
797 author = {Eric Jones and Travis Oliphant and Pearu Peterson and others},
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
798 title = {{SciPy}: Open source scientific tools for {Python}},
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
799 year = {2001--},
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
800 url = "http://www.scipy.org/",
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
801 note = {[Online; accessed 2016-04-09]}
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
802 }
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
803 </citation>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
804 </citations>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
805 </xml>
6fc9c7852ee4 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
806
5
01fdef045550 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
807 </macros>