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annotate feature_selection.xml @ 33:e918f33f7d4f draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8850f42c2c3763e614f7454c9c006f3d2ff572c0
author bgruening
date Fri, 27 May 2022 11:29:05 +0000
parents 93f3b307485f
children 61edd9e5c17f
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93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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1 <tool id="sklearn_feature_selection" name="Feature Selection" version="@VERSION@" profile="20.05">
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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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34 from galaxy_ml.utils import (SafeEval, feature_selector,
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35 read_columns, get_module)
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38 warnings.simplefilter('ignore')
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40 safe_eval = SafeEval()
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41
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42 input_json_path = sys.argv[1]
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43 with open(input_json_path, 'r') as param_handler:
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44 params = json.load(param_handler)
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46 ## handle cheetah
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47 #if $fs_algorithm_selector.selected_algorithm == 'SelectFromModel'\
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48 and $fs_algorithm_selector.model_inputter.input_mode == 'prefitted':
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49 params['fs_algorithm_selector']['model_inputter']['fitted_estimator'] =\
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50 '$fs_algorithm_selector.model_inputter.fitted_estimator'
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51 #end if
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53 #if $fs_algorithm_selector.selected_algorithm == 'SelectFromModel'\
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54 and $fs_algorithm_selector.model_inputter.input_mode == 'new'\
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55 and $fs_algorithm_selector.model_inputter.estimator_selector.selected_module == 'custom_estimator':
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56 params['fs_algorithm_selector']['model_inputter']['estimator_selector']['c_estimator'] =\
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57 '$fs_algorithm_selector.model_inputter.estimator_selector.c_estimator'
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58 #end if
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59
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60 #if $fs_algorithm_selector.selected_algorithm in ['RFE', 'RFECV', 'DyRFECV']\
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61 and $fs_algorithm_selector.estimator_selector.selected_module == 'custom_estimator':
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62 params['fs_algorithm_selector']['estimator_selector']['c_estimator'] =\
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63 '$fs_algorithm_selector.estimator_selector.c_estimator'
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64 #end if
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65
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66 #if $fs_algorithm_selector.selected_algorithm in ['RFECV', 'DyRFECV']\
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67 and $fs_algorithm_selector.options.cv_selector.selected_cv\
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68 in ['GroupKFold', 'GroupShuffleSplit', 'LeaveOneGroupOut', 'LeavePGroupsOut']:
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69 params['fs_algorithm_selector']['options']['cv_selector']['groups_selector']['infile_g'] =\
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70 '$fs_algorithm_selector.options.cv_selector.groups_selector.infile_g'
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71 #end if
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72
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73 ## Read features
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74 features_has_header = params['input_options']['header1']
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75 #if $input_options.selected_input == 'tabular'
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76 header = 'infer' if features_has_header else None
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77 column_option = params['input_options']['column_selector_options_1']['selected_column_selector_option']
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78 if column_option in ['by_index_number', 'all_but_by_index_number', 'by_header_name', 'all_but_by_header_name']:
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79 c = params['input_options']['column_selector_options_1']['col1']
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80 else:
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81 c = None
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82 X, input_df = read_columns(
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83 '$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)
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91 #elif $input_options.selected_input == 'seq_fasta'
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92 fasta_file = '$input_options.fasta_file'
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93 pyfaidx = get_module('pyfaidx')
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94 sequences = pyfaidx.Fasta(fasta_file)
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95 n_seqs = len(sequences.keys())
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96 X = np.arange(n_seqs)[:, np.newaxis]
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97 for param in estimator_params.keys():
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98 if param.endswith('fasta_path'):
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99 estimator.set_params(
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100 **{param: fasta_file})
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101 else:
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102 raise ValueError(
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103 "The selected estimator doesn't support "
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104 "fasta file input! Please consider using "
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105 "KerasGBatchClassifier with "
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106 "FastaDNABatchGenerator/FastaProteinBatchGenerator "
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107 "or having GenomeOneHotEncoder/ProteinOneHotEncoder "
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108 "in pipeline!")
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109 #elif $input_options.selected_input == 'sparse'
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110 X = mmread('$input_options.infile1')
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111 #end if
0
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112
18
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113 ## Read labels
17
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114 header = 'infer' if params['input_options']['header2'] else None
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115 column_option = params['input_options']['column_selector_options_2']['selected_column_selector_option2']
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116 if column_option in ['by_index_number', 'all_but_by_index_number', 'by_header_name', 'all_but_by_header_name']:
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117 c = params['input_options']['column_selector_options_2']['col2']
4
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118 else:
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119 c = None
0
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120 y = read_columns(
17
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121 '$input_options.infile2',
4
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122 c = c,
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123 c_option = column_option,
0
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124 sep='\t',
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125 header=header,
18
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126 parse_dates=True)
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127 y = y.ravel()
0
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128
18
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129 ## Create feature selector
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130 new_selector = feature_selector(params['fs_algorithm_selector'], X=X, y=y)
10
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131 if params['fs_algorithm_selector']['selected_algorithm'] != 'SelectFromModel'\
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132 or params['fs_algorithm_selector']['model_inputter']['input_mode'] != 'prefitted' :
2
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133 new_selector.fit(X, y)
0
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134
2
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135 ## Transform to select features
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136 selected_names = None
0
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137
17
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138 res = new_selector.transform(X)
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139 if features_has_header:
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140 selected_names = input_df.columns[new_selector.get_support(indices=True)]
2
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141 res = pandas.DataFrame(res, columns = selected_names)
17
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142 res.to_csv(path_or_buf='$outfile', sep='\t', index=False)
0
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143
17
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144 #if $save:
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145 with open('$outfile_selector', 'wb') as output_handler:
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146 pickle.dump(new_selector, output_handler, pickle.HIGHEST_PROTOCOL)
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147 #end if
0
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148
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149 ]]>
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150 </configfile>
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151 </configfiles>
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152 <inputs>
29
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153 <expand macro="feature_selection_fs" />
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154 <param name="save" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Save the fitted selector?" />
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155 <expand macro="sl_mixed_input_plus_sequence" />
0
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156 </inputs>
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157 <outputs>
17
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158 <data format="tabular" name="outfile" />
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159 <data format="zip" name="outfile_selector" label="${fs_algorithm_selector.selected_algorithm}">
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160 <filter>save</filter>
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161 </data>
0
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162 </outputs>
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163 <tests>
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164 <test>
29
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165 <param name="selected_algorithm" value="SelectFromModel" />
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166 <param name="input_mode" value="new" />
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167 <param name="selected_module" value="ensemble" />
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168 <param name="selected_estimator" value="RandomForestRegressor" />
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169 <param name="text_params" value="n_estimators=10, random_state=10" />
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170 <param name="infile1" value="regression_train.tabular" ftype="tabular" />
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171 <param name="header1" value="false" />
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172 <param name="col1" value="1,2,3,4,5" />
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173 <param name="infile2" value="regression_train.tabular" ftype="tabular" />
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174 <param name="col2" value="6" />
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175 <param name="header2" value="false" />
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176 <output name="outfile" file="feature_selection_result01" />
0
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177 </test>
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178 <test>
29
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
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179 <param name="selected_algorithm" value="GenericUnivariateSelect" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
180 <param name="param" value="20" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
181 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
182 <param name="header1" value="True" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
183 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
184 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
185 <param name="col2" value="1" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
186 <param name="header2" value="True" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
187 <output name="outfile" file="feature_selection_result02" />
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
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188 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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189 <test>
29
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
190 <param name="selected_algorithm" value="SelectPercentile" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
191 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
192 <param name="header1" value="True" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
193 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
194 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
195 <param name="col2" value="1" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
196 <param name="header2" value="True" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
197 <output name="outfile" file="feature_selection_result03" />
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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198 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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199 <test>
29
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
200 <param name="selected_algorithm" value="SelectKBest" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
201 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
202 <param name="header1" value="True" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
203 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
204 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
205 <param name="col2" value="1" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
206 <param name="header2" value="True" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
207 <output name="outfile" file="feature_selection_result04" />
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
208 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
209 <test>
29
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
210 <param name="selected_algorithm" value="SelectFpr" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
211 <param name="alpha" value="0.05" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
212 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
213 <param name="header1" value="True" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
214 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
215 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
216 <param name="col2" value="1" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
217 <param name="header2" value="True" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
218 <output name="outfile" file="feature_selection_result05" />
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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219 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
220 <test>
29
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
221 <param name="selected_algorithm" value="SelectFdr" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
222 <param name="alpha" value="0.05" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
223 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
224 <param name="header1" value="True" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
225 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
226 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
227 <param name="col2" value="1" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
228 <param name="header2" value="True" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
229 <output name="outfile" file="feature_selection_result06" />
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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230 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
231 <test>
29
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
232 <param name="selected_algorithm" value="SelectFwe" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
233 <param name="alpha" value="0.05" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
234 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
235 <param name="header1" value="True" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
236 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
237 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
238 <param name="col2" value="1" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
239 <param name="header2" value="True" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
240 <output name="outfile" file="feature_selection_result07" />
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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241 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
242 <test>
29
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
243 <param name="selected_algorithm" value="RFE" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
244 <param name="input_mode" value="new" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
245 <param name="selected_module" value="ensemble" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
246 <param name="selected_estimator" value="RandomForestRegressor" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
247 <param name="text_params" value="n_estimators=10, random_state=10" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
248 <param name="infile1" value="regression_train.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
249 <param name="header1" value="false" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
250 <param name="col1" value="1,2,3,4,5" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
251 <param name="infile2" value="regression_train.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
252 <param name="col2" value="6" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
253 <param name="header2" value="false" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
254 <output name="outfile" file="feature_selection_result08" />
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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255 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
256 <test>
29
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
257 <param name="selected_algorithm" value="RFECV" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
258 <param name="input_mode" value="new" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
259 <param name="selected_module" value="ensemble" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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260 <param name="selected_estimator" value="RandomForestRegressor" />
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261 <param name="text_params" value="n_estimators=10, random_state=10" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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262 <param name="infile1" value="regression_train.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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263 <param name="header1" value="false" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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264 <param name="col1" value="1,2,3,4,5" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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265 <param name="infile2" value="regression_train.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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266 <param name="col2" value="6" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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267 <param name="header2" value="false" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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268 <output name="outfile" file="feature_selection_result09" />
0
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269 </test>
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270 <test>
29
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271 <param name="selected_algorithm" value="VarianceThreshold" />
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272 <param name="threshold" value="0.1" />
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273 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
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274 <param name="header1" value="True" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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275 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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276 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
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277 <param name="col2" value="1" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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278 <param name="header2" value="True" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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279 <output name="outfile" file="feature_selection_result10" />
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280 </test>
6
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281 <test>
29
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282 <param name="selected_algorithm" value="SelectKBest" />
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283 <param name="k" value="3" />
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284 <param name="infile1" value="test3.tabular" ftype="tabular" />
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285 <param name="header1" value="True" />
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286 <param name="selected_column_selector_option" value="all_but_by_header_name" />
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287 <param name="col1" value="target" />
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288 <param name="infile2" value="test3.tabular" ftype="tabular" />
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289 <param name="header2" value="True" />
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290 <param name="selected_column_selector_option2" value="by_header_name" />
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291 <param name="col2" value="target" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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292 <output name="outfile" file="feature_selection_result11" />
6
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293 </test>
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294 <test>
29
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295 <param name="selected_algorithm" value="SelectFromModel" />
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296 <param name="input_mode" value="prefitted" />
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297 <param name="fitted_estimator" value="rfr_model01" ftype="zip" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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298 <param name="infile1" value="regression_train.tabular" ftype="tabular" />
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299 <param name="header1" value="false" />
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300 <param name="col1" value="1,2,3,4,5" />
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301 <param name="infile2" value="regression_train.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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302 <param name="col2" value="1" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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303 <param name="header2" value="false" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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304 <output name="outfile" file="feature_selection_result12" />
10
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305 </test>
18
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306 <test>
29
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307 <param name="selected_algorithm" value="RFECV" />
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308 <param name="input_mode" value="new" />
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309 <param name="selected_module" value="ensemble" />
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310 <param name="selected_estimator" value="RandomForestRegressor" />
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311 <param name="text_params" value="n_estimators=10, random_state=10" />
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312 <section name="groups_selector">
29
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313 <param name="infile_groups" value="regression_y.tabular" ftype="tabular" />
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314 <param name="header_g" value="true" />
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315 <param name="selected_column_selector_option_g" value="by_index_number" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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316 <param name="col_g" value="1" />
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317 </section>
29
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318 <param name="selected_cv" value="GroupShuffleSplit" />
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319 <param name="random_state" value="0" />
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320 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
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321 <param name="header1" value="true" />
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322 <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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323 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
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324 <param name="col2" value="1" />
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325 <param name="header2" value="true" />
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326 <output name="outfile" file="feature_selection_result13" />
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327 </test>
0
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328 </tests>
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329 <help>
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330 <![CDATA[
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331 **What it does**
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332 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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333 sklearn.metrics package.
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334 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
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335
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336 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
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337 ]]>
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338 </help>
14
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339 <expand macro="sklearn_citation">
29
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340 <expand macro="skrebate_citation" />
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341 <expand macro="xgboost_citation" />
14
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342 </expand>
0
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343 </tool>