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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 18:17:57 -0400
parents 2bbbac61e48d
children 0b88494bdcac
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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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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')
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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
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101 y = read_columns(
17
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102 '$input_options.infile2',
4
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103 c = c,
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104 c_option = column_option,
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105 sep='\t',
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106 header=header,
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107 parse_dates=True)
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108 y = y.ravel()
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109
18
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110 ## Create feature selector
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111 new_selector = feature_selector(params['fs_algorithm_selector'], X=X, y=y)
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112 if params['fs_algorithm_selector']['selected_algorithm'] != 'SelectFromModel'\
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113 or params['fs_algorithm_selector']['model_inputter']['input_mode'] != 'prefitted' :
2
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114 new_selector.fit(X, y)
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115
2
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116 ## Transform to select features
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117 selected_names = None
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118
17
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119 res = new_selector.transform(X)
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120 if features_has_header:
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121 selected_names = input_df.columns[new_selector.get_support(indices=True)]
2
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122 res = pandas.DataFrame(res, columns = selected_names)
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123 res.to_csv(path_or_buf='$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?"/>
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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"/>
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182 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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183 <param name="header1" value="True"/>
092199a095dd 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"/>
092199a095dd 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"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
186 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
187 <param name="header2" value="True"/>
092199a095dd 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"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
189 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
190 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
191 <param name="selected_algorithm" value="SelectFpr"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
192 <param name="alpha" value="0.05"/>
092199a095dd 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"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
194 <param name="header1" value="True"/>
092199a095dd 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"/>
092199a095dd 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"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
197 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
198 <param name="header2" value="True"/>
092199a095dd 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"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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200 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
201 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
202 <param name="selected_algorithm" value="SelectFdr"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
203 <param name="alpha" value="0.05"/>
092199a095dd 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"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
205 <param name="header1" value="True"/>
092199a095dd 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"/>
092199a095dd 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"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
208 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
209 <param name="header2" value="True"/>
092199a095dd 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"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
211 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
212 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
213 <param name="selected_algorithm" value="SelectFwe"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
214 <param name="alpha" value="0.05"/>
092199a095dd 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"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
216 <param name="header1" value="True"/>
092199a095dd 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"/>
092199a095dd 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"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
219 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
220 <param name="header2" value="True"/>
092199a095dd 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"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
222 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
223 <test>
092199a095dd 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
96f9b73327f2 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"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
226 <param name="selected_module" value="ensemble"/>
96f9b73327f2 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
f8dfdb47508b 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
96f9b73327f2 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"/>
96f9b73327f2 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"/>
96f9b73327f2 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"/>
96f9b73327f2 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"/>
96f9b73327f2 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"/>
96f9b73327f2 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
092199a095dd 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"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
236 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
237 <test>
092199a095dd 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
96f9b73327f2 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"/>
96f9b73327f2 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"/>
96f9b73327f2 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
f8dfdb47508b 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
96f9b73327f2 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"/>
96f9b73327f2 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"/>
96f9b73327f2 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"/>
96f9b73327f2 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"/>
96f9b73327f2 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"/>
96f9b73327f2 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
092199a095dd 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"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
250 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
251 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
252 <param name="selected_algorithm" value="VarianceThreshold"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
253 <param name="threshold" value="0.1"/>
092199a095dd 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"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
255 <param name="header1" value="True"/>
092199a095dd 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"/>
092199a095dd 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"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
258 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
259 <param name="header2" value="True"/>
092199a095dd 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"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
261 </test>
6
b0d554b38770 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents: 5
diff changeset
262 <test>
b0d554b38770 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"/>
b0d554b38770 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"/>
b0d554b38770 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"/>
b0d554b38770 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"/>
b0d554b38770 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"/>
b0d554b38770 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents: 5
diff changeset
268 <param name="col1" value="target"/>
b0d554b38770 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"/>
b0d554b38770 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents: 5
diff changeset
270 <param name="header2" value="True"/>
b0d554b38770 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents: 5
diff changeset
271 <param name="selected_column_selector_option2" value="by_header_name"/>
b0d554b38770 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents: 5
diff changeset
272 <param name="col2" value="target"/>
b0d554b38770 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
parents: 5
diff changeset
273 <output name="outfile" file="feature_selection_result11"/>
b0d554b38770 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
bgruening
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diff changeset
274 </test>
10
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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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>