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annotate feature_selection.xml @ 18:15d8ba35c23c draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
author bgruening
date Tue, 14 May 2019 17:50:10 -0400
parents cc5b841f040b
children 547fb1cde4cc
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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 <!--TODO: Add imblearn package support-->
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8 <expand macro="macro_stdio"/>
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9 <version_command>echo "@VERSION@"</version_command>
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10 <command>
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11 <![CDATA[
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12 python "$feature_selection_script" '$inputs'
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13 ]]>
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14 </command>
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15 <configfiles>
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16 <inputs name="inputs" />
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17 <configfile name="feature_selection_script">
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18 <![CDATA[
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19 import json
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20 import sklearn.feature_selection
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21 import skrebate
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22 import pandas
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23 import sys
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24 import warnings
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25 import xgboost
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26 from sklearn import (
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27 cluster, compose, decomposition, ensemble, feature_extraction,
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28 feature_selection, gaussian_process, kernel_approximation, metrics,
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29 model_selection, naive_bayes, neighbors, pipeline, preprocessing,
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30 svm, linear_model, tree, discriminant_analysis)
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31 from imblearn.pipeline import Pipeline as imbPipeline
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32 from sklearn.pipeline import Pipeline
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33
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34 sys.path.insert(0, '$__tool_directory__')
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35 from utils import SafeEval, feature_selector, read_columns
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37 warnings.simplefilter('ignore')
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39 safe_eval = SafeEval()
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40
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41 input_json_path = sys.argv[1]
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42 with open(input_json_path, 'r') as param_handler:
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43 params = json.load(param_handler)
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44
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45 ## handle cheetah
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46 #if $fs_algorithm_selector.selected_algorithm == 'SelectFromModel'\
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47 and $fs_algorithm_selector.model_inputter.input_mode == 'prefitted':
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48 params['fs_algorithm_selector']['model_inputter']['fitted_estimator'] =\
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49 '$fs_algorithm_selector.model_inputter.fitted_estimator'
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50 #end if
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51
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52 #if $fs_algorithm_selector.selected_algorithm == 'SelectFromModel'\
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53 and $fs_algorithm_selector.model_inputter.input_mode == 'new'\
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54 and $fs_algorithm_selector.model_inputter.estimator_selector.selected_module == 'custom_estimator':
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55 params['fs_algorithm_selector']['model_inputter']['estimator_selector']['c_estimator'] =\
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56 '$fs_algorithm_selector.model_inputter.estimator_selector.c_estimator'
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57 #end if
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58
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59 #if $fs_algorithm_selector.selected_algorithm in ['RFE', 'RFECV', 'DyRFECV']\
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60 and $fs_algorithm_selector.estimator_selector.selected_module == 'custom_estimator':
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61 params['fs_algorithm_selector']['estimator_selector']['c_estimator'] =\
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62 '$fs_algorithm_selector.estimator_selector.c_estimator'
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63 #end if
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64
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65 #if $fs_algorithm_selector.selected_algorithm in ['RFECV', 'DyRFECV']\
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66 and $fs_algorithm_selector.options.cv_selector.selected_cv\
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67 in ['GroupKFold', 'GroupShuffleSplit', 'LeaveOneGroupOut', 'LeavePGroupsOut']:
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68 params['fs_algorithm_selector']['options']['cv_selector']['groups_selector']['infile_g'] =\
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69 '$fs_algorithm_selector.options.cv_selector.groups_selector.infile_g'
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70 #end if
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71
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72 ## Read features
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73 features_has_header = params['input_options']['header1']
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74 input_type = params['input_options']['selected_input']
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75 if input_type == 'tabular':
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76 header = 'infer' if features_has_header else None
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77 column_option = params['input_options']['column_selector_options_1']['selected_column_selector_option']
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78 if column_option in ['by_index_number', 'all_but_by_index_number', 'by_header_name', 'all_but_by_header_name']:
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79 c = params['input_options']['column_selector_options_1']['col1']
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80 else:
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81 c = None
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82 X, input_df = read_columns(
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83 '$input_options.infile1',
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84 c = c,
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85 c_option = column_option,
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86 return_df = True,
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87 sep='\t',
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88 header=header,
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89 parse_dates=True)
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90 X = X.astype(float)
0
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91 else:
17
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92 X = mmread('$input_options.infile1')
0
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93
18
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94 ## Read labels
17
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95 header = 'infer' if params['input_options']['header2'] else None
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96 column_option = params['input_options']['column_selector_options_2']['selected_column_selector_option2']
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97 if column_option in ['by_index_number', 'all_but_by_index_number', 'by_header_name', 'all_but_by_header_name']:
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98 c = params['input_options']['column_selector_options_2']['col2']
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99 else:
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100 c = None
0
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101 y = read_columns(
17
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102 '$input_options.infile2',
4
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103 c = c,
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104 c_option = column_option,
0
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105 sep='\t',
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106 header=header,
18
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107 parse_dates=True)
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108 y = y.ravel()
0
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109
18
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110 ## Create feature selector
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111 new_selector = feature_selector(params['fs_algorithm_selector'], X=X, y=y)
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112 if params['fs_algorithm_selector']['selected_algorithm'] != 'SelectFromModel'\
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113 or params['fs_algorithm_selector']['model_inputter']['input_mode'] != 'prefitted' :
2
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114 new_selector.fit(X, y)
0
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115
2
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116 ## Transform to select features
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117 selected_names = None
0
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118
17
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119 res = new_selector.transform(X)
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120 if features_has_header:
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121 selected_names = input_df.columns[new_selector.get_support(indices=True)]
2
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122 res = pandas.DataFrame(res, columns = selected_names)
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123 res.to_csv(path_or_buf='$outfile', sep='\t', index=False)
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124
17
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125 #if $save:
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126 with open('$outfile_selector', 'wb') as output_handler:
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127 pickle.dump(new_selector, output_handler, pickle.HIGHEST_PROTOCOL)
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128 #end if
0
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129
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130 ]]>
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131 </configfile>
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132 </configfiles>
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133 <inputs>
17
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134 <expand macro="feature_selection_fs"/>
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135 <param name="save" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Save the fitted selector?"/>
0
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136 <expand macro="sl_mixed_input"/>
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137 </inputs>
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138 <outputs>
17
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139 <data format="tabular" name="outfile" />
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140 <data format="zip" name="outfile_selector" label="${fs_algorithm_selector.selected_algorithm}">
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141 <filter>save</filter>
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142 </data>
0
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143 </outputs>
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144 <tests>
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145 <test>
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146 <param name="selected_algorithm" value="SelectFromModel"/>
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147 <param name="input_mode" value="new"/>
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148 <param name="selected_module" value="ensemble"/>
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149 <param name="selected_estimator" value="RandomForestRegressor"/>
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150 <param name="text_params" value="n_estimators=10, random_state=10"/>
10
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151 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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152 <param name="header1" value="false"/>
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153 <param name="col1" value="1,2,3,4,5"/>
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154 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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155 <param name="col2" value="6"/>
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156 <param name="header2" value="false"/>
0
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157 <output name="outfile" file="feature_selection_result01"/>
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158 </test>
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159 <test>
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160 <param name="selected_algorithm" value="GenericUnivariateSelect"/>
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161 <param name="param" value="20"/>
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162 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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163 <param name="header1" value="True"/>
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164 <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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165 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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166 <param name="col2" value="1"/>
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167 <param name="header2" value="True"/>
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168 <output name="outfile" file="feature_selection_result02"/>
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169 </test>
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170 <test>
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171 <param name="selected_algorithm" value="SelectPercentile"/>
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172 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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173 <param name="header1" value="True"/>
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174 <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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175 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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176 <param name="col2" value="1"/>
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177 <param name="header2" value="True"/>
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178 <output name="outfile" file="feature_selection_result03"/>
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179 </test>
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180 <test>
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181 <param name="selected_algorithm" value="SelectKBest"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
182 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
183 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
184 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
185 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
186 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
187 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
188 <output name="outfile" file="feature_selection_result04"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
189 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
190 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
191 <param name="selected_algorithm" value="SelectFpr"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
192 <param name="alpha" value="0.05"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
193 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
194 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
195 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
196 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
197 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
198 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
199 <output name="outfile" file="feature_selection_result05"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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200 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
201 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
202 <param name="selected_algorithm" value="SelectFdr"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
203 <param name="alpha" value="0.05"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
204 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
205 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
206 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
207 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
208 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
209 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
210 <output name="outfile" file="feature_selection_result06"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
211 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
212 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
213 <param name="selected_algorithm" value="SelectFwe"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
214 <param name="alpha" value="0.05"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
215 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
216 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
217 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
218 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
219 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
220 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
221 <output name="outfile" file="feature_selection_result07"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
222 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
223 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
224 <param name="selected_algorithm" value="RFE"/>
10
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
225 <param name="input_mode" value="new"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
226 <param name="selected_module" value="ensemble"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
227 <param name="selected_estimator" value="RandomForestRegressor"/>
13
467550472f7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 10
diff changeset
228 <param name="text_params" value="n_estimators=10, random_state=10"/>
10
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
229 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
230 <param name="header1" value="false"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
231 <param name="col1" value="1,2,3,4,5"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
232 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
233 <param name="col2" value="6"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
234 <param name="header2" value="false"/>
0
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
235 <output name="outfile" file="feature_selection_result08"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
236 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
237 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
238 <param name="selected_algorithm" value="RFECV"/>
10
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
239 <param name="input_mode" value="new"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
240 <param name="selected_module" value="ensemble"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
241 <param name="selected_estimator" value="RandomForestRegressor"/>
13
467550472f7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 10
diff changeset
242 <param name="text_params" value="n_estimators=10, random_state=10"/>
10
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
243 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
244 <param name="header1" value="false"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
245 <param name="col1" value="1,2,3,4,5"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
246 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
247 <param name="col2" value="6"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
248 <param name="header2" value="false"/>
0
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
249 <output name="outfile" file="feature_selection_result09"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
250 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
251 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
252 <param name="selected_algorithm" value="VarianceThreshold"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
253 <param name="threshold" value="0.1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
254 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
255 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
256 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
257 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
258 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
259 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
260 <output name="outfile" file="feature_selection_result10"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
261 </test>
6
dc574d9778bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents: 5
diff changeset
262 <test>
dc574d9778bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents: 5
diff changeset
263 <param name="selected_algorithm" value="SelectKBest"/>
dc574d9778bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents: 5
diff changeset
264 <param name="k" value="3"/>
dc574d9778bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents: 5
diff changeset
265 <param name="infile1" value="test3.tabular" ftype="tabular"/>
dc574d9778bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents: 5
diff changeset
266 <param name="header1" value="True"/>
dc574d9778bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents: 5
diff changeset
267 <param name="selected_column_selector_option" value="all_but_by_header_name"/>
dc574d9778bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
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diff changeset
268 <param name="col1" value="target"/>
dc574d9778bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents: 5
diff changeset
269 <param name="infile2" value="test3.tabular" ftype="tabular"/>
dc574d9778bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
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diff changeset
270 <param name="header2" value="True"/>
dc574d9778bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
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271 <param name="selected_column_selector_option2" value="by_header_name"/>
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272 <param name="col2" value="target"/>
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273 <output name="outfile" file="feature_selection_result11"/>
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274 </test>
10
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275 <test>
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276 <param name="selected_algorithm" value="SelectFromModel"/>
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277 <param name="input_mode" value="prefitted"/>
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278 <param name="fitted_estimator" value="rfr_model01" ftype="zip"/>
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279 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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280 <param name="header1" value="false"/>
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281 <param name="col1" value="1,2,3,4,5"/>
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282 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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283 <param name="col2" value="1"/>
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284 <param name="header2" value="false"/>
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285 <output name="outfile" file="feature_selection_result12"/>
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286 </test>
18
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287 <test>
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288 <param name="selected_algorithm" value="RFECV"/>
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289 <param name="input_mode" value="new"/>
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290 <param name="selected_module" value="ensemble"/>
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291 <param name="selected_estimator" value="RandomForestRegressor"/>
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292 <param name="text_params" value="n_estimators=10, random_state=10"/>
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293 <section name="groups_selector">
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294 <param name="infile_groups" value="regression_y.tabular" ftype="tabular"/>
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295 <param name="header_g" value="true"/>
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296 <param name="selected_column_selector_option_g" value="by_index_number"/>
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297 <param name="col_g" value="1"/>
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298 </section>
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299 <param name="selected_cv" value="GroupShuffleSplit"/>
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300 <param name="random_state" value="0"/>
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301 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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302 <param name="header1" value="true"/>
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303 <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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304 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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305 <param name="col2" value="1"/>
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306 <param name="header2" value="true"/>
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307 <output name="outfile" file="feature_selection_result13"/>
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308 </test>
0
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309 </tests>
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310 <help>
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311 <![CDATA[
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312 **What it does**
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313 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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314 sklearn.metrics package.
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315 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
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316
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317 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
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318 ]]>
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319 </help>
14
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320 <expand macro="sklearn_citation">
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321 <expand macro="skrebate_citation"/>
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322 <expand macro="xgboost_citation"/>
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323 </expand>
0
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324 </tool>