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annotate feature_selection.xml @ 35:61edd9e5c17f draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
author bgruening
date Wed, 09 Aug 2023 13:10:57 +0000
parents 93f3b307485f
children
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35
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1 <tool id="sklearn_feature_selection" name="Feature Selection" version="@VERSION@" profile="@PROFILE@">
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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.model_persist import dump_model_to_h5
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35 from galaxy_ml.utils import (SafeEval, feature_selector,
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36 read_columns, get_module)
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39 warnings.simplefilter('ignore')
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41 safe_eval = SafeEval()
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42
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43 input_json_path = sys.argv[1]
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44 with open(input_json_path, 'r') as param_handler:
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45 params = json.load(param_handler)
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46
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47 ## handle cheetah
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48 #if $fs_algorithm_selector.selected_algorithm == 'SelectFromModel'\
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49 and $fs_algorithm_selector.model_inputter.input_mode == 'prefitted':
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50 params['fs_algorithm_selector']['model_inputter']['fitted_estimator'] =\
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51 '$fs_algorithm_selector.model_inputter.fitted_estimator'
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52 #end if
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53
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54 #if $fs_algorithm_selector.selected_algorithm == 'SelectFromModel'\
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55 and $fs_algorithm_selector.model_inputter.input_mode == 'new'\
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56 and $fs_algorithm_selector.model_inputter.estimator_selector.selected_module == 'custom_estimator':
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57 params['fs_algorithm_selector']['model_inputter']['estimator_selector']['c_estimator'] =\
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58 '$fs_algorithm_selector.model_inputter.estimator_selector.c_estimator'
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59 #end if
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60
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61 #if $fs_algorithm_selector.selected_algorithm in ['RFE', 'RFECV', 'DyRFECV']\
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62 and $fs_algorithm_selector.estimator_selector.selected_module == 'custom_estimator':
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63 params['fs_algorithm_selector']['estimator_selector']['c_estimator'] =\
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64 '$fs_algorithm_selector.estimator_selector.c_estimator'
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65 #end if
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66
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67 #if $fs_algorithm_selector.selected_algorithm in ['RFECV', 'DyRFECV']\
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68 and $fs_algorithm_selector.options.cv_selector.selected_cv\
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69 in ['GroupKFold', 'GroupShuffleSplit', 'LeaveOneGroupOut', 'LeavePGroupsOut']:
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70 params['fs_algorithm_selector']['options']['cv_selector']['groups_selector']['infile_g'] =\
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71 '$fs_algorithm_selector.options.cv_selector.groups_selector.infile_g'
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72 #end if
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73
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74 ## Read features
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75 features_has_header = params['input_options']['header1']
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76 #if $input_options.selected_input == 'tabular'
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77 header = 'infer' if features_has_header else None
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78 column_option = params['input_options']['column_selector_options_1']['selected_column_selector_option']
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79 if column_option in ['by_index_number', 'all_but_by_index_number', 'by_header_name', 'all_but_by_header_name']:
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80 c = params['input_options']['column_selector_options_1']['col1']
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81 else:
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82 c = None
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83 X, input_df = read_columns(
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84 '$input_options.infile1',
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85 c = c,
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86 c_option = column_option,
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87 return_df = True,
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88 sep='\t',
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89 header=header,
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90 parse_dates=True,
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91 )
20
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92 X = X.astype(float)
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93 #elif $input_options.selected_input == 'seq_fasta'
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94 fasta_file = '$input_options.fasta_file'
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95 pyfaidx = get_module('pyfaidx')
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96 sequences = pyfaidx.Fasta(fasta_file)
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97 n_seqs = len(sequences.keys())
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98 X = np.arange(n_seqs)[:, np.newaxis]
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99 for param in estimator_params.keys():
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100 if param.endswith('fasta_path'):
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101 estimator.set_params(
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102 **{param: fasta_file})
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103 else:
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104 raise ValueError(
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105 "The selected estimator doesn't support "
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106 "fasta file input! Please consider using "
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107 "KerasGBatchClassifier with "
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108 "FastaDNABatchGenerator/FastaProteinBatchGenerator "
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109 "or having GenomeOneHotEncoder/ProteinOneHotEncoder "
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110 "in pipeline!")
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111 #elif $input_options.selected_input == 'sparse'
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112 X = mmread('$input_options.infile1')
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113 #end if
0
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114
18
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115 ## Read labels
17
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116 header = 'infer' if params['input_options']['header2'] else None
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117 column_option = params['input_options']['column_selector_options_2']['selected_column_selector_option2']
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118 if column_option in ['by_index_number', 'all_but_by_index_number', 'by_header_name', 'all_but_by_header_name']:
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119 c = params['input_options']['column_selector_options_2']['col2']
4
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120 else:
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121 c = None
0
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122 y = read_columns(
35
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123 '$input_options.infile2',
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124 c = c,
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125 c_option = column_option,
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126 sep='\t',
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127 header=header,
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128 parse_dates=True,
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129 )
18
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130 y = y.ravel()
0
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131
18
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132 ## Create feature selector
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133 new_selector = feature_selector(params['fs_algorithm_selector'], X=X, y=y)
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134 if params['fs_algorithm_selector']['selected_algorithm'] != 'SelectFromModel'\
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135 or params['fs_algorithm_selector']['model_inputter']['input_mode'] != 'prefitted' :
2
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136 new_selector.fit(X, y)
0
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137
2
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138 ## Transform to select features
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139 selected_names = None
0
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140
17
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141 res = new_selector.transform(X)
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142 if features_has_header:
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143 selected_names = input_df.columns[new_selector.get_support(indices=True)]
2
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144 res = pandas.DataFrame(res, columns = selected_names)
17
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145 res.to_csv(path_or_buf='$outfile', sep='\t', index=False)
0
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146
17
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147 #if $save:
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148 dump_model_to_h5(new_selector, '$outfile_selector')
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149 #end if
0
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150
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151 ]]>
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152 </configfile>
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153 </configfiles>
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154 <inputs>
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155 <expand macro="feature_selection_fs" />
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156 <param name="save" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Save the fitted selector?" />
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157 <expand macro="sl_mixed_input_plus_sequence" />
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158 </inputs>
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159 <outputs>
17
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160 <data format="tabular" name="outfile" />
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161 <data format="h5mlm" name="outfile_selector" label="${fs_algorithm_selector.selected_algorithm}">
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162 <filter>save</filter>
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163 </data>
0
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164 </outputs>
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165 <tests>
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166 <test>
29
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167 <param name="selected_algorithm" value="SelectFromModel" />
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168 <param name="input_mode" value="new" />
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169 <param name="selected_module" value="ensemble" />
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170 <param name="selected_estimator" value="RandomForestRegressor" />
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171 <param name="text_params" value="n_estimators=10, random_state=10" />
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172 <param name="infile1" value="regression_train.tabular" ftype="tabular" />
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173 <param name="header1" value="false" />
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174 <param name="col1" value="1,2,3,4,5" />
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175 <param name="infile2" value="regression_train.tabular" ftype="tabular" />
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176 <param name="col2" value="6" />
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177 <param name="header2" value="false" />
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178 <output name="outfile" file="feature_selection_result01" />
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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179 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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180 <test>
29
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
181 <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
182 <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
183 <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
184 <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
185 <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
186 <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
187 <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
188 <param name="header2" value="True" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
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189 <output name="outfile" file="feature_selection_result02" />
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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190 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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191 <test>
29
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
192 <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
193 <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
194 <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
195 <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
196 <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
197 <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
198 <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
199 <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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200 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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201 <test>
29
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
202 <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
203 <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
204 <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
205 <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
206 <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
207 <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
208 <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
209 <output name="outfile" file="feature_selection_result04" />
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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210 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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211 <test>
29
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
212 <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
213 <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
214 <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
215 <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
216 <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
217 <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
218 <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
219 <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
220 <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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221 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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222 <test>
29
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
223 <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
224 <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
225 <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
226 <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
227 <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
228 <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
229 <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
230 <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
231 <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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232 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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233 <test>
29
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
234 <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
235 <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
236 <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
237 <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
238 <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
239 <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
240 <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
241 <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
242 <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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243 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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244 <test>
29
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_algorithm" value="RFE" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
diff changeset
246 <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
247 <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
248 <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
249 <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
250 <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
251 <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
252 <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
253 <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
254 <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
255 <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
256 <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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257 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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258 <test>
29
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_algorithm" value="RFECV" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 22
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260 <param name="input_mode" value="new" />
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261 <param name="selected_module" value="ensemble" />
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262 <param name="selected_estimator" value="RandomForestRegressor" />
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263 <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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264 <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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265 <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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266 <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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267 <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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268 <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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269 <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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270 <output name="outfile" file="feature_selection_result09" />
0
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271 </test>
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272 <test>
29
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273 <param name="selected_algorithm" value="VarianceThreshold" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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274 <param name="threshold" value="0.1" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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275 <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"
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276 <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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277 <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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278 <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"
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279 <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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280 <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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281 <output name="outfile" file="feature_selection_result10" />
0
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282 </test>
6
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283 <test>
29
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284 <param name="selected_algorithm" value="SelectKBest" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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285 <param name="k" value="3" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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286 <param name="infile1" value="test3.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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287 <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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288 <param name="selected_column_selector_option" value="all_but_by_header_name" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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289 <param name="col1" value="target" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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290 <param name="infile2" value="test3.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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291 <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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292 <param name="selected_column_selector_option2" value="by_header_name" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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293 <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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294 <output name="outfile" file="feature_selection_result11" />
6
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295 </test>
10
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296 <test>
29
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297 <param name="selected_algorithm" value="SelectFromModel" />
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298 <param name="input_mode" value="prefitted" />
35
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299 <param name="fitted_estimator" value="searchCV03" ftype="h5mlm" />
61edd9e5c17f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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300 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
61edd9e5c17f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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301 <param name="header1" value="true" />
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302 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
61edd9e5c17f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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303 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
29
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304 <param name="col2" value="1" />
35
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305 <param name="header2" value="true" />
29
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306 <output name="outfile" file="feature_selection_result12" />
10
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307 </test>
18
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308 <test>
29
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309 <param name="selected_algorithm" value="RFECV" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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310 <param name="input_mode" value="new" />
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311 <param name="selected_module" value="ensemble" />
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312 <param name="selected_estimator" value="RandomForestRegressor" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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313 <param name="text_params" value="n_estimators=10, random_state=10" />
18
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314 <section name="groups_selector">
29
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315 <param name="infile_groups" value="regression_y.tabular" ftype="tabular" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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316 <param name="header_g" value="true" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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317 <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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318 <param name="col_g" value="1" />
18
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319 </section>
29
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320 <param name="selected_cv" value="GroupShuffleSplit" />
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321 <param name="random_state" value="0" />
93f3b307485f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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322 <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"
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323 <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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324 <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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325 <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"
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326 <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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327 <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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328 <output name="outfile" file="feature_selection_result13" />
18
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329 </test>
0
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330 </tests>
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331 <help>
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332 <![CDATA[
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333 **What it does**
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334 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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335 sklearn.metrics package.
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336 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
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337
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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338 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
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339 ]]>
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340 </help>
14
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341 <expand macro="sklearn_citation">
29
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342 <expand macro="skrebate_citation" />
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343 <expand macro="xgboost_citation" />
14
dc411a215138 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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344 </expand>
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092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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345 </tool>