Mercurial > repos > bgruening > sklearn_feature_selection

annotate feature_selection.xml @ 26:a0ae33c96077 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
author bgruening
date Wed, 22 Jan 2020 12:17:59 +0000
parents bfdf732091c1
children 2ac77e0aec82
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1 <tool id="sklearn_feature_selection" name="Feature Selection" version="@VERSION@">
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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 from galaxy_ml.utils import (SafeEval, feature_selector,
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35 read_columns, get_module)
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36
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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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45
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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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52
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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 '$input_options.infile2',
4
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122 c = c,
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123 c_option = column_option,
0
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124 sep='\t',
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125 header=header,
18
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126 parse_dates=True)
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127 y = y.ravel()
0
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128
18
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129 ## Create feature selector
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130 new_selector = feature_selector(params['fs_algorithm_selector'], X=X, y=y)
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131 if params['fs_algorithm_selector']['selected_algorithm'] != 'SelectFromModel'\
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132 or params['fs_algorithm_selector']['model_inputter']['input_mode'] != 'prefitted' :
2
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133 new_selector.fit(X, y)
0
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134
2
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135 ## Transform to select features
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136 selected_names = None
0
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137
17
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138 res = new_selector.transform(X)
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139 if features_has_header:
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140 selected_names = input_df.columns[new_selector.get_support(indices=True)]
2
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141 res = pandas.DataFrame(res, columns = selected_names)
17
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142 res.to_csv(path_or_buf='$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>
17
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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>
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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"/>
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"/>
0
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176 <output name="outfile" file="feature_selection_result01"/>
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177 </test>
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178 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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179 <param name="selected_algorithm" value="GenericUnivariateSelect"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
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180 <param name="param" value="20"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
181 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
182 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
183 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
184 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
185 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
186 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
187 <output name="outfile" file="feature_selection_result02"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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188 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
189 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
190 <param name="selected_algorithm" value="SelectPercentile"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
191 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
192 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
193 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
194 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
195 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
196 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
197 <output name="outfile" file="feature_selection_result03"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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198 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
199 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
200 <param name="selected_algorithm" value="SelectKBest"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
201 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
202 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
203 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
204 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
205 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
206 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
207 <output name="outfile" file="feature_selection_result04"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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208 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
209 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
210 <param name="selected_algorithm" value="SelectFpr"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
211 <param name="alpha" value="0.05"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
212 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
213 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
214 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
215 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
216 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
217 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
218 <output name="outfile" file="feature_selection_result05"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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219 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
220 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
221 <param name="selected_algorithm" value="SelectFdr"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
222 <param name="alpha" value="0.05"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
223 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
224 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
225 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
226 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
227 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
228 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
229 <output name="outfile" file="feature_selection_result06"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
230 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
231 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
232 <param name="selected_algorithm" value="SelectFwe"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
233 <param name="alpha" value="0.05"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
234 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
235 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
236 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
237 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
238 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
239 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
240 <output name="outfile" file="feature_selection_result07"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
241 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
242 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
243 <param name="selected_algorithm" value="RFE"/>
10
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
244 <param name="input_mode" value="new"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
245 <param name="selected_module" value="ensemble"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
246 <param name="selected_estimator" value="RandomForestRegressor"/>
13
467550472f7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
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diff changeset
247 <param name="text_params" value="n_estimators=10, random_state=10"/>
10
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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diff changeset
248 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
249 <param name="header1" value="false"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
250 <param name="col1" value="1,2,3,4,5"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
251 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
252 <param name="col2" value="6"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
253 <param name="header2" value="false"/>
0
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
254 <output name="outfile" file="feature_selection_result08"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
255 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
256 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
257 <param name="selected_algorithm" value="RFECV"/>
10
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
258 <param name="input_mode" value="new"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
259 <param name="selected_module" value="ensemble"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
260 <param name="selected_estimator" value="RandomForestRegressor"/>
13
467550472f7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 10
diff changeset
261 <param name="text_params" value="n_estimators=10, random_state=10"/>
10
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
262 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
263 <param name="header1" value="false"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
264 <param name="col1" value="1,2,3,4,5"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
265 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
266 <param name="col2" value="6"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
parents: 9
diff changeset
267 <param name="header2" value="false"/>
0
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
268 <output name="outfile" file="feature_selection_result09"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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269 </test>
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270 <test>
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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"/>
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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"/>
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276 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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277 <param name="col2" value="1"/>
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278 <param name="header2" value="True"/>
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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>
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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"/>
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292 <output name="outfile" file="feature_selection_result11"/>
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293 </test>
10
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294 <test>
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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"/>
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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"/>
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302 <param name="col2" value="1"/>
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303 <param name="header2" value="false"/>
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304 <output name="outfile" file="feature_selection_result12"/>
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305 </test>
18
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306 <test>
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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">
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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"/>
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316 <param name="col_g" value="1"/>
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317 </section>
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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">
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340 <expand macro="skrebate_citation"/>
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341 <expand macro="xgboost_citation"/>
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342 </expand>
0
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343 </tool>