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annotate main_macros.xml @ 4:c85acc0197c6 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
author bgruening
date Thu, 23 Jun 2016 15:26:05 -0400
parents cd3e98b58c1e
children 25a68adb2ade
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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@">
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5 def columns(f,c):
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6 data = pandas.read_csv(f, sep='\t', header=None, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False)
c85acc0197c6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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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
c85acc0197c6 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991
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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="0.2.1b">eden</requirement>
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17 <yield />
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18 </requirements>
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19 </xml>
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20
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21 <xml name="macro_stdio">
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22 <stdio>
3
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23 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
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24 </stdio>
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25 </xml>
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26
2
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27
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28 <!--Generic interface-->
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29 <xml name="train_loadConditional" token_train="tabular" token_data="tabular" token_model="txt">
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30 <conditional name="selected_tasks">
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31 <param name="selected_task" type="select" label="Select a Classification Task">
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32 <option value="train" selected="true">Train a model</option>
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33 <option value="load">Load a model and predict</option>
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34 </param>
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35 <when value="load">
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36 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/>
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37 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
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38 <conditional name="prediction_options">
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39 <param name="prediction_option" type="select" label="Select the type of prediction">
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40 <option value="predict">Predict class labels</option>
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41 <option value="advanced">Include advanced options</option>
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42 </param>
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43 <when value="predict">
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44 </when>
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45 <when value="advanced">
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46 </when>
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47 </conditional>
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48 </when>
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49 <when value="train">
3
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50 <param name="infile_train" type="data" format="@TRAIN@" label="Training samples (tabular)"/>
0
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51 <conditional name="selected_algorithms">
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52 <yield />
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53 </conditional>
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54 </when>
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55 </conditional>
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56 </xml>
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57
2
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58 <xml name="sl_Conditional" token_train="tabular" token_data="tabular" token_model="txt">
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59 <conditional name="selected_tasks">
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60 <param name="selected_task" type="select" label="Select a Classification Task">
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61 <option value="train" selected="true">Train a model</option>
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62 <option value="load">Load a model and predict</option>
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63 </param>
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64 <when value="load">
3
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65 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/>
2
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66 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
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67 <conditional name="prediction_options">
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68 <param name="prediction_option" type="select" label="Select the type of prediction">
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69 <option value="predict">Predict class labels</option>
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70 <option value="advanced">Include advanced options</option>
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71 </param>
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72 <when value="predict">
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73 </when>
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74 <when value="advanced">
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75 </when>
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76 </conditional>
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77 </when>
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78 <when value="train">
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79 <conditional name="selected_algorithms">
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80 <yield />
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81 </conditional>
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82 </when>
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83 </conditional>
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84 </xml>
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85
0
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86 <xml name="advanced_section">
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87 <section name="options" title="Advanced Options" expanded="False">
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88 <yield />
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89 </section>
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90 </xml>
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91
2
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92
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93 <!--Ensemble methods-->
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94 <xml name="n_estimators" token_default_value="10" token_help=" ">
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95 <param argument="n_estimators" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of trees in the forest" help="@HELP@"/>
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96 </xml>
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97
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98 <xml name="max_depth" token_default_value="" token_help=" ">
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99 <param argument="max_depth" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@"/>
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100 </xml>
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101
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102 <xml name="min_samples_split" token_default_value="2" token_help=" ">
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103 <param argument="min_samples_split" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@"/>
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104 </xml>
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105
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106 <xml name="min_samples_leaf" token_default_value="1" token_help=" ">
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107 <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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108 </xml>
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109
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110 <xml name="min_weight_fraction_leaf" token_default_value="0.0" token_help=" ">
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111 <param argument="min_weight_fraction_leaf" type="float" optional="true" value="@DEFAULT_VALUE@" label="Minimum weighted fraction of the input samples required to be at a leaf node" help="@HELP@"/>
0
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112 </xml>
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113
2
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114 <xml name="max_leaf_nodes" token_default_value="" token_help=" ">
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115 <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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116 </xml>
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117
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118 <xml name="bootstrap" token_checked="true" token_help=" ">
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119 <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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120 </xml>
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121
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122 <xml name="criterion" token_help=" ">
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123 <param argument="criterion" type="select" label="Function to measure the quality of a split" help=" ">
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124 <option value="gini" selected="true">Gini impurity</option>
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125 <option value="entropy">Information gain</option>
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126 <yield/>
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127 </param>
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128 </xml>
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129
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130 <xml name="oob_score" token_checked="flase" token_help=" ">
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131 <param argument="oob_score" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Use out-of-bag samples to estimate the generalization error" help="@HELP@"/>
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132 </xml>
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133
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134 <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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135 <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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136 </xml>
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137
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138 <xml name="learning_rate" token_default_value="1.0" token_help=" ">
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139 <param argument="learning_rate" type="float" optional="true" value="@DEFAULT_VALUE@" label="Learning rate" help="@HELP@"/>
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140 </xml>
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141
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142
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143 <!--Parameters-->
0
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144 <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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145 <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@"/>
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146 </xml>
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147
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148 <xml name="n_clusters" token_default_value="8">
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149 <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" "/>
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150 </xml>
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151
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152 <xml name="fit_intercept" token_checked="true">
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153 <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Estimate the intercept" help="If false, the data is assumed to be already centered."/>
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154 </xml>
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155
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156 <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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157 <param argument="n_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@"/>
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158 </xml>
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159
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160 <xml name="shuffle" token_checked="true" token_help_text=" " token_label="Shuffle data after each iteration">
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161 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="@LABEL@" help="@HELP_TEXT@"/>
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162 </xml>
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163
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164 <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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165 <param argument="random_state" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Random seed number" help="@HELP_TEXT@"/>
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166 </xml>
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167
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168 <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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169 <param argument="warm_start" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Perform warm start" help="@HELP_TEXT@"/>
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170 </xml>
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171
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172 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term.">
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173 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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174 </xml>
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175
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176 <!--xml name="class_weight" token_default_value="" token_help_text="">
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177 <param argument="class_weight" type="" optional="true" value="@DEFAULT_VALUE@" label="" help="@HELP_TEXT@"/>
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178 </xml-->
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179
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180 <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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181 <param argument="alpha" type="float" optional="true" value="@DEFAULT_VALUE@" label="Regularization coefficient" help="@HELP_TEXT@"/>
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182 </xml>
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183
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184 <xml name="n_samples" token_default_value="100" token_help_text="The total number of points equally divided among clusters.">
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185 <param argument="n_samples" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of samples" help="@HELP_TEXT@"/>
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186 </xml>
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187
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188 <xml name="n_features" token_default_value="2" token_help_text="Number of different numerical properties produced for each sample.">
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189 <param argument="n_features" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of features" help="@HELP_TEXT@"/>
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190 </xml>
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191
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192 <xml name="noise" token_default_value="0.0" token_help_text="Floating point number. ">
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193 <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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194 </xml>
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195
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196 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term. ">
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197 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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198 </xml>
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199
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200 <xml name="max_iter" token_default_value="300" token_label="Maximum number of iterations per single run" token_help_text=" ">
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201 <param argument="max_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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202 </xml>
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203
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204 <xml name="n_init" token_default_value="10" >
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205 <param argument="n_init" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of runs with different centroid seeds" help=" "/>
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206 </xml>
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207
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208 <xml name="init">
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209 <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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210 <option value="k-means++">k-means++</option>
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211 <option value="random">random</option>
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212 </param>
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213 </xml>
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214
1
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215 <xml name="gamma" token_default_value="1.0" token_label="Scaling parameter" token_help_text=" ">
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216 <param argument="gamma" type="float" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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217 </xml>
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218
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219 <xml name="degree" token_default_value="3" token_label="Degree of the polynomial" token_help_text=" ">
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220 <param argument="degree" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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221 </xml>
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222
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223 <xml name="coef0" token_default_value="1" token_label="Zero coefficient" token_help_text=" ">
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224 <param argument="coef0" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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225 </xml>
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226
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227 <xml name="pos_label" token_default_value="">
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228 <param argument="pos_label" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Label of the positive class" help=" "/>
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229 </xml>
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230
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231 <xml name="average">
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232 <param argument="average" type="select" optional="true" label="Averaging type" help=" ">
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233 <option value="micro" help="Calculate metrics globally by counting the total true positives, false negatives and false positives.">micro</option>
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234 <option value="samples" help="Calculate metrics for each instance, and find their average (only meaningful for multilabel).">samples</option>
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235 <!--option value="macro" help=""></option-->
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236 <!--option value="weighted" help=""></option-->
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237 <yield/>
2
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238 </param>
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239 </xml>
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240
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241 <xml name="beta">
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242 <param argument="beta" type="float" value="1.0" label="The strength of recall versus precision in the F-score" help=" "/>
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243 </xml>
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244
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245
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246 <!--Data interface-->
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247 <xml name="tabular_input">
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248 <param name="infile" type="data" format="tabular" label="Data file with numeric values"/>
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249 <param name="start_column" type="data_column" data_ref="infile" optional="True" label="Select a subset of data. Start column:" />
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250 <param name="end_column" type="data_column" data_ref="infile" optional="True" label="End column:" />
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251 </xml>
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252
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253 <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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254 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
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255 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/>
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256 <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/>
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257 <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
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258 <yield/>
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259 </xml>
1
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260
4
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261
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262 <xml name="clf_inputs_extended" token_label1=" " token_label2=" " token_multiple="False">
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263 <conditional name="true_columns">
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264 <param name="selected_input1" type="select" label="Select the input type of true labels dataset:">
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265 <option value="tabular" selected="true">Tabular</option>
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266 <option value="sparse">Sparse</option>
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267 </param>
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268 <when value="tabular">
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269 <param name="infile1" type="data" label="@LABEL1@"/>
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270 <param name="col1" type="data_column" data_ref="infile1" label="Select the target column:"/>
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271 </when>
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272 <when value="sparse">
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273 <param name="infile1" type="data" format="txt" label="@LABEL1@"/>
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274 </when>
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275 </conditional>
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276 <conditional name="predicted_columns">
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277 <param name="selected_input2" type="select" label="Select the input type of predicted labels dataset:">
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278 <option value="tabular" selected="true">Tabular</option>
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279 <option value="sparse">Sparse</option>
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280 </param>
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281 <when value="tabular">
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282 <param name="infile2" type="data" label="@LABEL2@"/>
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283 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
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284 </when>
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285 <when value="sparse">
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286 <param name="infile2" type="data" format="txt" label="@LABEL1@"/>
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287 </when>
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288 </conditional>
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289 </xml>
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290
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291 <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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292 <param name="infile1" type="data" format="tabular" label="@LABEL1@"/>
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293 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select the target column:"/>
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294 <param name="infile2" type="data" format="tabular" label="@LABEL2@"/>
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295 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
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296 </xml>
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297
1
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298 <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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299 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):">
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300 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/>
0
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301 </repeat>
2
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302 </xml>
0
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303
2
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304 <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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305 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
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306 <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/>
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307 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
0
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308 </xml>
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309
2
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310 <xml name="sl_mixed_input">
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311 <conditional name="input_options">
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312 <param name="selected_input" type="select" label="Select input type:">
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313 <option value="tabular" selected="true">tabular data</option>
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314 <option value="sparse">sparse matrix</option>
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315 </param>
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316 <when value="tabular">
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317 <expand macro="sample_cols" multiple1="true"/>
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318 </when>
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319 <when value="sparse">
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320 <expand macro="sparse_target"/>
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321 </when>
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322 </conditional>
0
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323 </xml>
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324
3
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325 <xml name="multitype_input" token_format="tabular" token_help="All datasets with tabular format are supporetd.">
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326 <param name="infile_transform" type="data" format="@FORMAT@" label="Select a dataset to transform:" help="@HELP@"/>
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327 </xml>
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328
0
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329
2
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330 <!--Advanced options-->
0
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331 <xml name="nn_advanced_options">
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332 <section name="options" title="Advanced Options" expanded="False">
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333 <yield/>
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334 <param argument="weights" type="select" label="Weight function" help="Used in prediction.">
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335 <option value="uniform" selected="true" help="Uniform weights. All points in each neighborhood are weighted equally.">Uniform</option>
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336 <option value="distance" help="Weight points by the inverse of their distance.">Distance</option>
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337 </param>
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338 <param argument="algorithm" type="select" label="Neighbor selection algorithm" help=" ">
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339 <option value="auto" selected="true">Auto</option>
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340 <option value="ball_tree">BallTree</option>
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341 <option value="kd_tree">KDTree</option>
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342 <option value="brute">Brute-force</option>
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343 </param>
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344 <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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345 <!--param name="metric"-->
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346 <!--param name="p"-->
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347 <!--param name="metric_params"-->
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348 </section>
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349 </xml>
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350
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351 <xml name="svc_advanced_options">
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352 <section name="options" title="Advanced Options" expanded="False">
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353 <yield/>
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354 <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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355 <option value="rbf" selected="true">rbf</option>
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356 <option value="linear">linear</option>
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357 <option value="poly">poly</option>
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358 <option value="sigmoid">sigmoid</option>
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359 <option value="precomputed">precomputed</option>
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360 </param>
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361 <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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362 <!--TODO: param argument="gamma" float, optional (default=’auto’) -->
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363 <param argument="coef0" type="float" optional="true" value="0.0" label="Zero coefficient (polynomial and sigmoid kernels only)" help="Independent term in kernel function. dafault: 0.0 "/>
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364 <param argument="shrinking" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use the shrinking heuristic" help=" "/>
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365 <param argument="probability" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Enable probability estimates. " help="This must be enabled prior to calling fit, and will slow down that method."/>
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366 <!-- param argument="cache_size"-->
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367 <!--expand macro="class_weight"/-->
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368 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. "/>
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369 <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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370 <!--param argument="decision_function_shape"-->
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371 <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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372 </section>
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373 </xml>
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374
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375 <xml name="spectral_clustering_advanced_options">
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376 <section name="options" title="Advanced Options" expanded="False">
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377 <expand macro="n_clusters"/>
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378 <param argument="eigen_solver" type="select" value="" label="Eigen solver" help="The eigenvalue decomposition strategy to use.">
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379 <option value="arpack" selected="true">arpack</option>
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380 <option value="lobpcg">lobpcg</option>
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381 <option value="amg">amg</option>
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382 <!--None-->
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383 </param>
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384 <expand macro="random_state"/>
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385 <expand macro="n_init"/>
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386 <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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387 <param argument="affinity" type="select" label="Affinity" help="Affinity kernel to use. ">
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388 <option value="rbf" selected="true">RBF</option>
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389 <option value="precomputed">precomputed</option>
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390 <option value="nearest_neighbors">Nearset neighbors</option>
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391 </param>
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392 <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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393 <!--param argument="eigen_tol"-->
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394 <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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395 <option value="kmeans" selected="true">kmeans</option>
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396 <option value="discretize">discretize</option>
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397 </param>
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398 <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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399 <param argument="coef0" type="integer" optional="true" value="1" label="Zero coefficient (polynomial and sigmoid kernels only)" help="Ignored by other kernels. dafault : 1 "/>
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400 <!--param argument="kernel_params"-->
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401 </section>
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402 </xml>
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403
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404 <xml name="minibatch_kmeans_advanced_options">
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405 <section name="options" title="Advanced Options" expanded="False">
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406 <expand macro="n_clusters"/>
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407 <expand macro="init"/>
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408 <expand macro="n_init" default_value="3"/>
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409 <expand macro="max_iter" default_value="100"/>
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410 <expand macro="tol" help_text="Early stopping heuristics based on normalized center change. To disable set to 0.0 ."/>
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411 <expand macro="random_state"/>
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412 <param argument="batch_size" type="integer" optional="true" value="100" label="Batch size" help="Size of the mini batches."/>
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413 <!--param argument="compute_labels"-->
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414 <param argument="max_no_improvement" type="integer" optional="true" value="10" label="Maximum number of improvement attempts" help="
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415 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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416 To disable, set max_no_improvement to None. "/>
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417 <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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418 <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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419 </section>
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420 </xml>
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421
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422 <xml name="kmeans_advanced_options">
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423 <section name="options" title="Advanced Options" expanded="False">
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424 <expand macro="n_clusters"/>
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425 <expand macro="init"/>
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426 <expand macro="n_init"/>
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427 <expand macro="max_iter"/>
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428 <expand macro="tol" default_value="0.0001" help_text="Relative tolerance with regards to inertia to declare convergence."/>
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429 <!--param argument="precompute_distances"/-->
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430 <expand macro="random_state"/>
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431 <param argument="copy_x" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing distances" help="Mofifying the original data introduces small numerical differences caused by subtracting and then adding the data mean."/>
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432 </section>
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433 </xml>
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434
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435 <xml name="birch_advanced_options">
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436 <section name="options" title="Advanced Options" expanded="False">
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437 <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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438 <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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439 <expand macro="n_clusters" default_value="3"/>
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440 <!--param argument="compute_labels"/-->
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441 </section>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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442 </xml>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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443
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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444 <xml name="dbscan_advanced_options">
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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445 <section name="options" title="Advanced Options" expanded="False">
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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446 <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."/>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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447 <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."/>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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448 <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."/>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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449 <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.">
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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450 <option value="auto" selected="true">auto</option>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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451 <option value="ball_tree">ball_tree</option>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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452 <option value="kd_tree">kd_tree</option>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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453 <option value="brute">brute</option>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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454 </param>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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455 <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."/>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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456 </section>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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457 </xml>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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458
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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459 <xml name="clustering_algorithms_options">
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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460 <conditional name="algorithm_options">
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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461 <param name="selected_algorithm" type="select" label="Clustering Algorithm">
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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462 <option value="KMeans" selected="true">KMeans</option>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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463 <option value="SpectralClustering">Spectral Clustering</option>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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464 <option value="MiniBatchKMeans">Mini Batch KMeans</option>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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465 <option value="DBSCAN">DBSCAN</option>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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466 <option value="Birch">Birch</option>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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467 </param>
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468 <when value="KMeans">
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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469 <expand macro="kmeans_advanced_options"/>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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470 </when>
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471 <when value="DBSCAN">
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
472 <expand macro="dbscan_advanced_options"/>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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473 </when>
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474 <when value="Birch">
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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475 <expand macro="birch_advanced_options"/>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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476 </when>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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diff changeset
477 <when value="SpectralClustering">
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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478 <expand macro="spectral_clustering_advanced_options"/>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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479 </when>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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480 <when value="MiniBatchKMeans">
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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481 <expand macro="minibatch_kmeans_advanced_options"/>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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482 </when>
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483 </conditional>
4354c286f7a7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a6e80305ed0892c8163d690a2d376d6b454824de-dirty
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484 </xml>
1
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parents: 0
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485
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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486 <xml name="distance_metrics">
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487 <param argument="metric" type="select" label="Distance metric" help=" ">
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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488 <option value="euclidean" selected="true">euclidean</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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diff changeset
489 <option value="cityblock">cityblock</option>
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490 <option value="cosine">cosine</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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diff changeset
491 <option value="l1">l1</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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diff changeset
492 <option value="l2">l2</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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493 <option value="manhattan">manhattan</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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diff changeset
494 <yield/>
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495 </param>
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496 </xml>
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497
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
498 <xml name="distance_nonsparse_metrics">
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499 <option value="braycurtis">braycurtis</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
500 <option value="canberra">canberra</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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501 <option value="chebyshev">chebyshev</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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diff changeset
502 <option value="correlation">correlation</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
503 <option value="dice">dice</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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diff changeset
504 <option value="hamming">hamming</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
505 <option value="jaccard">jaccard</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
506 <option value="kulsinski">kulsinski</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
507 <option value="mahalanobis">mahalanobis</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
508 <option value="matching">matching</option>
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bgruening
parents: 0
diff changeset
509 <option value="minkowski">minkowski</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
510 <option value="rogerstanimoto">rogerstanimoto</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
511 <option value="russellrao">russellrao</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
512 <option value="seuclidean">seuclidean</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
513 <option value="sokalmichener">sokalmichener</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
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514 <option value="sokalsneath">sokalsneath</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
515 <option value="sqeuclidean">sqeuclidean</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
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diff changeset
516 <option value="yule">yule</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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diff changeset
517 </xml>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
518
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
519 <xml name="pairwise_kernel_metrics">
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diff changeset
520 <param argument="metric" type="select" label="Pirwise Kernel metric" help=" ">
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
521 <option value="rbf" selected="true">rbf</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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diff changeset
522 <option value="sigmoid">sigmoid</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
523 <option value="polynomial">polynomial</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
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524 <option value="linear" selected="true">linear</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
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diff changeset
525 <option value="chi2">chi2</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
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526 <option value="additive_chi2">additive_chi2</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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diff changeset
527 </param>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
528 </xml>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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529
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
530 <xml name="sparse_pairwise_metric_functions">
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
531 <param name="selected_metric_function" type="select" label="Select the pairwise metric you want to compute:">
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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diff changeset
532 <option value="euclidean_distances" selected="true">Euclidean distance matrix</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
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533 <option value="pairwise_distances">Distance matrix</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
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parents: 0
diff changeset
534 <option value="pairwise_distances_argmin">Minimum distances between one point and a set of points</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
535 <yield/>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
536 </param>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
537 </xml>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
538
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
539 <xml name="pairwise_metric_functions">
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
540 <option value="additive_chi2_kernel" >Additive chi-squared kernel</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
541 <option value="chi2_kernel">Exponential chi-squared kernel</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
542 <option value="linear_kernel">Linear kernel</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
543 <option value="manhattan_distances">L1 distances</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
544 <option value="pairwise_kernels">Kernel</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
545 <option value="polynomial_kernel">Polynomial kernel</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
546 <option value="rbf_kernel">Gaussian (rbf) kernel</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
547 <option value="laplacian_kernel">Laplacian kernel</option>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
548 </xml>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
549
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
550 <xml name="sparse_pairwise_condition">
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
551 <when value="pairwise_distances">
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
552 <section name="options" title="Advanced Options" expanded="False">
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
553 <expand macro="distance_metrics">
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
554 <yield/>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
555 </expand>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
556 </section>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
557 </when>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
558 <when value="euclidean_distances">
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
559 <section name="options" title="Advanced Options" expanded="False">
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
560 <param argument="squared" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Return squared Euclidean distances" help=" "/>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
561 </section>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
562 </when>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
563 </xml>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
564
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
565 <xml name="argmin_distance_condition">
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
566 <when value="pairwise_distances_argmin">
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
567 <section name="options" title="Advanced Options" expanded="False">
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
568 <param argument="axis" type="integer" optional="true" value="1" label="Axis" help="Axis along which the argmin and distances are to be computed."/>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
569 <expand macro="distance_metrics">
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
570 <yield/>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
571 </expand>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
572 <param argument="batch_size" type="integer" optional="true" value="500" label="Batch size" help="Number of rows to be processed in each batch run."/>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
573 </section>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
574 </when>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
575 </xml>
ced78bc020cc planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents: 0
diff changeset
576
2
ebdb2e9fd1c7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
577 <xml name="sparse_preprocessors">
ebdb2e9fd1c7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
578 <param name="selected_pre_processor" type="select" label="Select a preprocessor:">
3
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
579 <option value="StandardScaler" selected="true">Standard Scaler (Standardizes features by removing the mean and scaling to unit variance)</option>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
580 <option value="Binarizer">Binarizer (Binarizes data)</option>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
581 <option value="Imputer">Imputer (Completes missing values)</option>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
582 <option value="MaxAbsScaler">Max Abs Scaler (Scales features by their maximum absolute value)</option>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
583 <option value="Normalizer">Normalizer (Normalizes samples individually to unit norm)</option>
2
ebdb2e9fd1c7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
584 <yield/>
ebdb2e9fd1c7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
585 </param>
ebdb2e9fd1c7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
586 </xml>
ebdb2e9fd1c7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
587
ebdb2e9fd1c7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
588 <xml name="sparse_preprocessor_options">
ebdb2e9fd1c7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
589 <when value="Binarizer">
3
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
590 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
2
ebdb2e9fd1c7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
591 <section name="options" title="Advanced Options" expanded="False">
3
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
592 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing binarization" help=" "/>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
593 <param argument="threshold" type="float" optional="true" value="0.0" label="Threshold" help="Feature values below or equal to this are replaced by 0, above it by 1. Threshold may not be less than 0 for operations on sparse matrices. "/>
2
ebdb2e9fd1c7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
594 </section>
ebdb2e9fd1c7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
595 </when>
ebdb2e9fd1c7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents: 1
diff changeset
596 <when value="Imputer">
3
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
597 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
598 <section name="options" title="Advanced Options" expanded="False">
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
599 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing imputation" help=" "/>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
600 <param argument="strategy" type="select" optional="true" label="Imputation strategy" help=" ">
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
601 <option value="mean" selected="true">Replace missing values using the mean along the axis</option>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
602 <option value="median">Replace missing values using the median along the axis</option>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
603 <option value="most_frequent">Replace missing using the most frequent value along the axis</option>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
604 </param>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
605 <param argument="missing_values" type="text" optional="true" value="NaN" label="Placeholder for missing values" help="For missing values encoded as numpy.nan, use the string value “NaN”"/>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
606 <param argument="axis" type="boolean" optional="true" truevalue="1" falsevalue="0" label="Impute along axis = 1" help="If fasle, axis = 0 is selected for imputation. "/>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
607 <!--param argument="axis" type="select" optional="true" label="The axis along which to impute" help=" ">
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
608 <option value="0" selected="true">Impute along columns</option>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
609 <option value="1">Impute along rows</option>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
610 </param-->
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
611 </section>
2
ebdb2e9fd1c7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
612 </when>
ebdb2e9fd1c7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
613 <when value="StandardScaler">
3
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
614 <expand macro="multitype_input"/>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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parents: 2
diff changeset
615 <section name="options" title="Advanced Options" expanded="False">
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
616 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for performing inplace scaling" help=" "/>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
617 <param argument="with_mean" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Center the data before scaling" help=" "/>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
618 <param argument="with_std" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Scale the data to unit variance (or unit standard deviation)" help=" "/>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
619 </section>
2
ebdb2e9fd1c7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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diff changeset
620 </when>
ebdb2e9fd1c7 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
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parents: 1
diff changeset
621 <when value="MaxAbsScaler">
3
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
622 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
bgruening
parents: 2
diff changeset
623 <section name="options" title="Advanced Options" expanded="False">
cd3e98b58c1e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a349cb4673231f12344e418513a08691925565d9
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diff changeset
624 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing scaling" help=" "/>
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625 </section>
2
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626 </when>
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627 <when value="Normalizer">
3
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628 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
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629 <section name="options" title="Advanced Options" expanded="False">
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630 <param argument="norm" type="select" optional="true" label="The norm to use to normalize non zero samples" help=" ">
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631 <option value="l1" selected="true">l1</option>
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632 <option value="l2">l2</option>
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633 <option value="max">max</option>
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634 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing row normalization" help=" "/>
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635 </param>
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636 </section>
2
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637 </when>
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638 <yield/>
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639 </xml>
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640
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641
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642 <!--Citations-->
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643 <xml name="eden_citation">
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644 <citations>
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645 <citation type="bibtex">
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646 @misc{fabrizio_costa_2015_15094,
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647 author = {Fabrizio Costa and
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648 Björn Grüning and
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649 gigolo},
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650 title = {EDeN: EDeN - Graph Vectorizer},
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651 month = feb,
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652 year = 2015,
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653 doi = {10.5281/zenodo.15094},
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654 url = {http://dx.doi.org/10.5281/zenodo.15094}
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655 }
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656 }
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657 </citation>
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658 </citations>
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659 </xml>
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660
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661 <xml name="sklearn_citation">
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662 <citations>
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663 <citation type="bibtex">
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664 @article{scikit-learn,
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665 title={Scikit-learn: Machine Learning in {P}ython},
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666 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
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667 and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
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668 and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
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669 Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
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670 journal={Journal of Machine Learning Research},
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671 volume={12},
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672 pages={2825--2830},
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673 year={2011}
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674 url = {https://github.com/scikit-learn/scikit-learn}
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675 }
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676 </citation>
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677 </citations>
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678 </xml>
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679
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680 <xml name="scipy_citation">
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681 <citations>
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682 <citation type="bibtex">
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683 @Misc{,
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684 author = {Eric Jones and Travis Oliphant and Pearu Peterson and others},
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685 title = {{SciPy}: Open source scientific tools for {Python}},
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686 year = {2001--},
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687 url = "http://www.scipy.org/",
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688 note = {[Online; accessed 2016-04-09]}
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689 }
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690 </citation>
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691 </citations>
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692 </xml>
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693
1
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694 </macros>