Mercurial > repos > bgruening > sklearn_feature_selection

annotate feature_selection.xml @ 11:9af844f24ef6 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977
author bgruening
date Sat, 04 Aug 2018 17:36:15 -0400
parents 96f9b73327f2
children f8dfdb47508b
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1 <tool id="sklearn_feature_selection" name="Feature Selection" version="@VERSION@.1">
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2 <description>module, including univariate filter selection methods and recursive feature elimination algorithm</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 </macros>
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6 <expand macro="python_requirements"/>
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7 <expand macro="macro_stdio"/>
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8 <version_command>echo "@VERSION@"</version_command>
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9 <command>
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10 <![CDATA[
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11 python "$feature_selection_script" '$inputs'
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12 ]]>
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13 </command>
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14 <configfiles>
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15 <inputs name="inputs" />
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16 <configfile name="feature_selection_script">
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17 <![CDATA[
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18 import sys
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19 import json
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20 import pandas
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21 import pickle
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22 import ast
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23 import numpy as np
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24 import xgboost
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25 import sklearn.feature_selection
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26 from sklearn import svm, linear_model, ensemble, naive_bayes, tree, neighbors
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27
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28 @COLUMNS_FUNCTION@
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29 @GET_ESTIMATOR_FUNCTION@
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30 @FEATURE_SELECTOR_FUNCTION@
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31
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32 input_json_path = sys.argv[1]
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33 with open(input_json_path, "r") as param_handler:
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34 params = json.load(param_handler)
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35
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36 #handle cheetah
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37 #if $fs_algorithm_selector.selected_algorithm == "SelectFromModel"\
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38 and $fs_algorithm_selector.model_inputter.input_mode == "prefitted":
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39 params['fs_algorithm_selector']['model_inputter']['fitted_estimator'] =\
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40 "$fs_algorithm_selector.model_inputter.fitted_estimator"
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41 #end if
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42
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43 # Read features
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44 features_has_header = params["input_options"]["header1"]
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45 input_type = params["input_options"]["selected_input"]
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46 if input_type=="tabular":
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47 header = 'infer' if features_has_header else None
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48 column_option = params["input_options"]["column_selector_options_1"]["selected_column_selector_option"]
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49 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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50 c = params["input_options"]["column_selector_options_1"]["col1"]
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51 else:
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52 c = None
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53 X, input_df = read_columns(
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54 "$input_options.infile1",
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55 c = c,
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56 c_option = column_option,
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57 return_df = True,
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58 sep='\t',
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59 header=header,
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60 parse_dates=True
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61 )
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62 else:
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63 X = mmread("$input_options.infile1")
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64
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65 # Read labels
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66 header = 'infer' if params["input_options"]["header2"] else None
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67 column_option = params["input_options"]["column_selector_options_2"]["selected_column_selector_option2"]
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68 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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69 c = params["input_options"]["column_selector_options_2"]["col2"]
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70 else:
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71 c = None
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72 y = read_columns(
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73 "$input_options.infile2",
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74 c = c,
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75 c_option = column_option,
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76 sep='\t',
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77 header=header,
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78 parse_dates=True
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79 )
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80 y=y.ravel()
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81
10
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82 # Create feature selector
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83 new_selector = feature_selector(params['fs_algorithm_selector'])
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84 if params['fs_algorithm_selector']['selected_algorithm'] != 'SelectFromModel'\
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85 or params['fs_algorithm_selector']['model_inputter']['input_mode'] != 'prefitted' :
2
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86 new_selector.fit(X, y)
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87
2
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88 ## Transform to select features
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89 selected_names = None
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90 if "$output_method_selector.selected_method" == "fit_transform":
2
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91 res = new_selector.transform(X)
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92 if features_has_header:
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93 selected_names = input_df.columns[new_selector.get_support(indices=True)]
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94 else:
10
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95 res = new_selector.get_support(params["output_method_selector"]["indices"])
0
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96
2
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97 res = pandas.DataFrame(res, columns = selected_names)
0
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98 res.to_csv(path_or_buf="$outfile", sep='\t', index=False)
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99
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100
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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101 ]]>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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102 </configfile>
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103 </configfiles>
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104 <inputs>
10
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105 <expand macro="feature_selection_all">
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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106 <expand macro="fs_selectfrommodel_prefitted"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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107 </expand>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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108 <expand macro="feature_selection_output_mothods" />
0
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109 <expand macro="sl_mixed_input"/>
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110 </inputs>
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111 <outputs>
2
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112 <data format="tabular" name="outfile"/>
0
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113 </outputs>
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114 <tests>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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115 <test>
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116 <param name="selected_algorithm" value="SelectFromModel"/>
10
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117 <param name="input_mode" value="new"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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118 <param name="selected_module" value="ensemble"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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119 <param name="selected_estimator" value="RandomForestRegressor"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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120 <param name="text_params" value="'n_estimators': 10, 'random_state': 10"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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121 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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122 <param name="header1" value="false"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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123 <param name="col1" value="1,2,3,4,5"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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124 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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125 <param name="col2" value="6"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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126 <param name="header2" value="false"/>
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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127 <output name="outfile" file="feature_selection_result01"/>
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128 </test>
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129 <test>
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130 <param name="selected_algorithm" value="GenericUnivariateSelect"/>
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131 <param name="param" value="20"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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132 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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133 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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134 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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135 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
136 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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137 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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138 <output name="outfile" file="feature_selection_result02"/>
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139 </test>
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140 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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141 <param name="selected_algorithm" value="SelectPercentile"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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142 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
143 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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144 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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145 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
146 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
147 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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148 <output name="outfile" file="feature_selection_result03"/>
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149 </test>
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150 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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151 <param name="selected_algorithm" value="SelectKBest"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
152 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
153 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
154 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
155 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
156 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
157 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
158 <output name="outfile" file="feature_selection_result04"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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159 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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160 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
161 <param name="selected_algorithm" value="SelectFpr"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
162 <param name="alpha" value="0.05"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
163 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
164 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
165 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
166 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
167 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
168 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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169 <output name="outfile" file="feature_selection_result05"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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170 </test>
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171 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
172 <param name="selected_algorithm" value="SelectFdr"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
173 <param name="alpha" value="0.05"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
174 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
175 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
176 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
177 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
178 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
179 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
180 <output name="outfile" file="feature_selection_result06"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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181 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
182 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
183 <param name="selected_algorithm" value="SelectFwe"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
184 <param name="alpha" value="0.05"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
185 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
186 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
187 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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188 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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189 <param name="col2" value="1"/>
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190 <param name="header2" value="True"/>
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191 <output name="outfile" file="feature_selection_result07"/>
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192 </test>
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193 <test>
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194 <param name="selected_algorithm" value="RFE"/>
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195 <param name="input_mode" value="new"/>
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196 <param name="selected_module" value="ensemble"/>
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197 <param name="selected_estimator" value="RandomForestRegressor"/>
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198 <param name="text_params" value="'n_estimators': 10, 'random_state':10"/>
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199 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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200 <param name="header1" value="false"/>
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201 <param name="col1" value="1,2,3,4,5"/>
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202 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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203 <param name="col2" value="6"/>
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204 <param name="header2" value="false"/>
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205 <output name="outfile" file="feature_selection_result08"/>
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206 </test>
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207 <test>
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208 <param name="selected_algorithm" value="RFECV"/>
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209 <param name="input_mode" value="new"/>
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210 <param name="selected_module" value="ensemble"/>
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211 <param name="selected_estimator" value="RandomForestRegressor"/>
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212 <param name="text_params" value="'n_estimators': 10, 'random_state':10"/>
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213 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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214 <param name="header1" value="false"/>
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215 <param name="col1" value="1,2,3,4,5"/>
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216 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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217 <param name="col2" value="6"/>
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218 <param name="header2" value="false"/>
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219 <output name="outfile" file="feature_selection_result09"/>
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220 </test>
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221 <test>
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222 <param name="selected_algorithm" value="VarianceThreshold"/>
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223 <param name="threshold" value="0.1"/>
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224 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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225 <param name="header1" value="True"/>
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226 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
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227 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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228 <param name="col2" value="1"/>
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229 <param name="header2" value="True"/>
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230 <output name="outfile" file="feature_selection_result10"/>
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231 </test>
6
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232 <test>
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233 <param name="selected_algorithm" value="SelectKBest"/>
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234 <param name="k" value="3"/>
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235 <param name="infile1" value="test3.tabular" ftype="tabular"/>
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236 <param name="header1" value="True"/>
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237 <param name="selected_column_selector_option" value="all_but_by_header_name"/>
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238 <param name="col1" value="target"/>
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239 <param name="infile2" value="test3.tabular" ftype="tabular"/>
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240 <param name="header2" value="True"/>
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241 <param name="selected_column_selector_option2" value="by_header_name"/>
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242 <param name="col2" value="target"/>
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243 <output name="outfile" file="feature_selection_result11"/>
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244 </test>
10
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245 <test>
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246 <param name="selected_algorithm" value="SelectFromModel"/>
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247 <param name="input_mode" value="prefitted"/>
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248 <param name="fitted_estimator" value="rfr_model01" ftype="zip"/>
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249 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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250 <param name="header1" value="false"/>
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251 <param name="col1" value="1,2,3,4,5"/>
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252 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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253 <param name="col2" value="1"/>
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254 <param name="header2" value="false"/>
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255 <output name="outfile" file="feature_selection_result12"/>
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256 </test>
0
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257 </tests>
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258 <help>
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259 <![CDATA[
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260 **What it does**
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261 This tool provides several loss, score, and utility functions to measure classification performance. Some metrics might require probability estimates of the positive class, confidence values, or binary decisions values. This tool is based on
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262 sklearn.metrics package.
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263 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
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264
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265 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
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266 ]]>
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267 </help>
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268 <expand macro="sklearn_citation"/>
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269 </tool>