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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
author bgruening
date Mon, 02 Oct 2023 09:21:02 +0000
parents 1fe00785190d
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1 <tool id="sklearn_model_validation" name="Model Validation" version="@VERSION@" profile="@PROFILE@">
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2 <description>includes cross_validate, cross_val_predict, learning_curve, and more</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 <expand macro="macro_stdio" />
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8 <version_command>echo "@VERSION@"</version_command>
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9 <command>
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10 <![CDATA[
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11 export HDF5_USE_FILE_LOCKING='FALSE';
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12 python "$sklearn_model_validation_script" '$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="sklearn_model_validation_script">
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18 <![CDATA[
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19 import imblearn
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20 import joblib
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21 import json
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22 import numpy as np
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23 import os
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24 import pandas as pd
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25 import pprint
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26 import skrebate
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27 import sys
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28 import warnings
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29 import xgboost
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30 from mlxtend import classifier, regressor
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31 from sklearn import (
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32 cluster, compose, decomposition, ensemble, feature_extraction,
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33 feature_selection, gaussian_process, kernel_approximation, metrics,
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34 model_selection, naive_bayes, neighbors, pipeline, preprocessing,
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35 svm, linear_model, tree, discriminant_analysis)
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36 from sklearn.model_selection import _validation
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37 from sklearn.preprocessing import LabelEncoder
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38
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39 from distutils.version import LooseVersion as Version
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40 from galaxy_ml import __version__ as galaxy_ml_version
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41 from galaxy_ml.model_persist import load_model_from_h5
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42 from galaxy_ml.utils import (SafeEval, get_cv, get_scoring,
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43 read_columns, get_module,
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44 clean_params, get_main_estimator)
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47 N_JOBS = int(os.environ.get('GALAXY_SLOTS', 1))
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48 CACHE_DIR = os.path.join(os.getcwd(), 'cached')
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50 warnings.filterwarnings('ignore')
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52 safe_eval = SafeEval()
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54 input_json_path = sys.argv[1]
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55 with open(input_json_path, 'r') as param_handler:
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56 params = json.load(param_handler)
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58 ## load estimator
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59 estimator = load_model_from_h5('$infile_estimator')
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60 estimator = clean_params(estimator)
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62 if estimator.__class__.__name__ == 'KerasGBatchClassifier':
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63 _fit_and_score = try_get_attr('galaxy_ml.model_validations',
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64 '_fit_and_score')
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66 setattr(_search, '_fit_and_score', _fit_and_score)
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67 setattr(_validation, '_fit_and_score', _fit_and_score)
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69 estimator_params = estimator.get_params()
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71 ## check estimator hyperparameters
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72 memory = joblib.Memory(location=CACHE_DIR, verbose=0)
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73 # cache iraps_core fits could increase search speed significantly
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74 if estimator.__class__.__name__ == 'IRAPSClassifier':
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75 estimator.set_params(memory=memory)
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76 else:
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77 # For iraps buried in pipeline
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78 for p, v in estimator_params.items():
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79 if p.endswith('__irapsclassifier__memory'):
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80 new_params = {p: memory}
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81 estimator.set_params(**new_params)
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83 ## store read dataframe object
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84 loaded_df = {}
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85
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86 #if $input_options.selected_input == 'tabular'
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87 header = 'infer' if params['input_options']['header1'] else None
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88 column_option = params['input_options']['column_selector_options_1']['selected_column_selector_option']
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89 if column_option in ['by_index_number', 'all_but_by_index_number', 'by_header_name', 'all_but_by_header_name']:
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90 c = params['input_options']['column_selector_options_1']['col1']
0
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91 else:
19
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92 c = None
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93 infile1 = '$input_options.infile1'
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94 df_key = infile1 + repr(header)
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95 df = pd.read_csv(infile1, sep='\t', header=header, parse_dates=True)
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96 loaded_df[df_key] = df
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97 X = read_columns(df, c=c, c_option=column_option).astype(float)
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98
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99 #elif $input_options.selected_input == 'sparse':
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100 X = mmread('$input_options.infile1')
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101
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102 #elif $input_options.selected_input == 'seq_fasta'
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103 fasta_path = '$input_options.fasta_path'
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104 pyfaidx = get_module('pyfaidx')
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105 sequences = pyfaidx.Fasta(fasta_path)
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106 n_seqs = len(sequences.keys())
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107 X = np.arange(n_seqs)[:, np.newaxis]
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108 for param in estimator_params.keys():
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109 if param.endswith('fasta_path'):
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110 estimator.set_params(
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111 **{param: fasta_path})
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112 break
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113 else:
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114 raise ValueError(
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115 "The selected estimator doesn't support "
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116 "fasta file input! Please consider using "
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117 "KerasGBatchClassifier with "
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118 "FastaDNABatchGenerator/FastaProteinBatchGenerator "
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119 "or having GenomeOneHotEncoder/ProteinOneHotEncoder "
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120 "in pipeline!")
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121 #elif $input_options.selected_input == 'refseq_and_interval'
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122 ref_seq = '$input_options.ref_genome_file'
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123 intervals = '$input_options.interval_file'
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124 targets = __import__('os').path.join(__import__('os').getcwd(),
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125 '${target_file.element_identifier}.gz')
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126 path_params = {
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127 'data_batch_generator__ref_genome_path': ref_seq,
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128 'data_batch_generator__intervals_path': intervals,
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129 'data_batch_generator__target_path': targets
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130 }
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131 estimator.set_params(**path_params)
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132 n_intervals = sum(1 for line in open(intervals))
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133 X = np.arange(n_intervals)[:, np.newaxis]
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134 #end if
0
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135
16
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136 header = 'infer' if params['input_options']['header2'] else None
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137 column_option = params['input_options']['column_selector_options_2']['selected_column_selector_option2']
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138 if column_option in ['by_index_number', 'all_but_by_index_number', 'by_header_name', 'all_but_by_header_name']:
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139 c = params['input_options']['column_selector_options_2']['col2']
3
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140 else:
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141 c = None
19
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142 infile2 = '$input_options.infile2'
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143 df_key = infile2 + repr(header)
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144 if df_key in loaded_df:
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145 infile2 = loaded_df[df_key]
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146 else:
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147 infile2 = pd.read_csv(infile2, sep='\t', header=header, parse_dates=True)
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148 loaded_df[df_key] = infile2
0
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149 y = read_columns(
34
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150 infile2,
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151 c = c,
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152 c_option = column_option,
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153 sep='\t',
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154 header=header,
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155 parse_dates=True)
19
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156 if len(y.shape) == 2 and y.shape[1] == 1:
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157 y = y.ravel()
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158 #if $input_options.selected_input == 'refseq_and_interval'
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159 estimator.set_params(
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160 data_batch_generator__features=y.ravel().tolist())
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161 y = None
34
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162 label_encoder = LabelEncoder()
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163 if get_main_estimator(estimator).__class__.__name__ == "XGBClassifier":
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164 y = label_encoder.fit_transform(y)
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165 print(label_encoder.classes_)
19
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166 #end if
0
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167
17
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168 ## handle options
16
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169 options = params['model_validation_functions']['options']
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170
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171 #if $model_validation_functions.options.cv_selector.selected_cv\
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172 in ['GroupKFold', 'GroupShuffleSplit', 'LeaveOneGroupOut', 'LeavePGroupsOut']:
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173 infile_g = '$model_validation_functions.options.cv_selector.groups_selector.infile_g'
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174 header = 'infer' if options['cv_selector']['groups_selector']['header_g'] else None
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175 column_option = (options['cv_selector']['groups_selector']['column_selector_options_g']
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176 ['selected_column_selector_option_g'])
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177 if column_option in ['by_index_number', 'all_but_by_index_number',
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178 'by_header_name', 'all_but_by_header_name']:
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179 c = (options['cv_selector']['groups_selector']['column_selector_options_g']['col_g'])
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180 else:
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181 c = None
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182 df_key = infile_g + repr(header)
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183 if df_key in loaded_df:
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184 infile_g = loaded_df[df_key]
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185 groups = read_columns(infile_g, c=c, c_option=column_option,
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186 sep='\t', header=header, parse_dates=True)
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187 groups = groups.ravel()
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188 options['cv_selector']['groups_selector'] = groups
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189 #end if
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190
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191 ## del loaded_df
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192 del loaded_df
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193
34
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194 cv_selector = options.pop('cv_selector')
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195 if Version(galaxy_ml_version) < Version('0.8.3'):
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196 cv_selector.pop('n_stratification_bins', None)
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197 splitter, groups = get_cv( cv_selector )
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198 options['cv'] = splitter
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199 options['groups'] = groups
12
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200 options['n_jobs'] = N_JOBS
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201 if 'scoring' in options:
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202 primary_scoring = options['scoring']['primary_scoring']
12
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203 options['scoring'] = get_scoring(options['scoring'])
2
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204 if 'pre_dispatch' in options and options['pre_dispatch'] == '':
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205 options['pre_dispatch'] = None
0
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206
19
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207 ## Set up validator, run estimator through validator and return results.
0
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208
16
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209 validator = params['model_validation_functions']['selected_function']
19
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210 validator = getattr(_validation, validator)
2
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211
16
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212 selected_function = params['model_validation_functions']['selected_function']
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213
2
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214 if selected_function == 'cross_validate':
19
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215 res = validator(estimator, X, y, **options)
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216 stat = {}
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217 for k, v in res.items():
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218 if k.startswith('test'):
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219 stat['mean_' + k] = np.mean(v)
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220 stat['std_' + k] = np.std(v)
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221 res.update(stat)
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222 rval = pd.DataFrame(res)
19
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223 rval = rval[sorted(rval.columns)]
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224 elif selected_function == 'cross_val_predict':
19
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225 predicted = validator(estimator, X, y, **options)
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226 if len(predicted.shape) == 1:
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227 rval = pd.DataFrame(predicted, columns=['Predicted'])
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228 else:
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229 rval = pd.DataFrame(predicted)
2
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230 elif selected_function == 'learning_curve':
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diff changeset
231 try:
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232 train_sizes = safe_eval(options['train_sizes'])
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233 except:
17
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234 sys.exit("Unsupported train_sizes input! Supports int/float in tuple and array-like structure.")
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235 if type(train_sizes) is tuple:
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236 train_sizes = np.linspace(*train_sizes)
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237 options['train_sizes'] = train_sizes
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238 train_sizes_abs, train_scores, test_scores = validator(estimator, X, y, **options)
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239 rval = pd.DataFrame(dict(
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240 train_sizes_abs = train_sizes_abs,
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241 mean_train_scores = np.mean(train_scores, axis=1),
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242 std_train_scores = np.std(train_scores, axis=1),
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243 mean_test_scores = np.mean(test_scores, axis=1),
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244 std_test_scores = np.std(test_scores, axis=1)))
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245 rval = rval[['train_sizes_abs', 'mean_train_scores', 'std_train_scores',
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246 'mean_test_scores', 'std_test_scores']]
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247 elif selected_function == 'permutation_test_score':
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248 score, permutation_scores, pvalue = validator(estimator, X, y, **options)
17
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249 permutation_scores_df = pd.DataFrame(dict(
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250 permutation_scores = permutation_scores))
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251 score_df = pd.DataFrame(dict(
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252 score = [score],
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253 pvalue = [pvalue]))
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254 rval = pd.concat([score_df[['score', 'pvalue']], permutation_scores_df], axis=1)
0
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255
17
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256 rval.to_csv(path_or_buf='$outfile', sep='\t', header=True, index=False)
0
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257
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258 ]]>
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259 </configfile>
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260 </configfiles>
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261 <inputs>
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262 <param name="infile_estimator" type="data" format="h5mlm" label="Choose the dataset containing model/pipeline object" />
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263 <conditional name="model_validation_functions">
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264 <param name="selected_function" type="select" label="Select a model validation function">
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265 <option value="cross_validate">cross_validate - Evaluate metric(s) by cross-validation and also record fit/score times</option>
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266 <option value="cross_val_predict">cross_val_predict - Generate cross-validated estimates for each input data point</option>
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267 <option value="learning_curve">learning_curve - Learning curve</option>
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268 <option value="permutation_test_score">permutation_test_score - Evaluate the significance of a cross-validated score with permutations</option>
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269 <option value="validation_curve">validation_curve - Use grid search with one parameter instead</option>
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270 </param>
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271 <when value="cross_validate">
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272 <section name="options" title="Other Options" expanded="false">
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273 <expand macro="scoring_selection" />
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274 <expand macro="model_validation_common_options" />
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275 <param argument="return_train_score" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" help="Whether to include train scores." />
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276 <!--param argument="return_estimator" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" help="Whether to return the estimators fitted on each split." /> -->
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277 <!--param argument="error_score" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Raise fit error:" help="If false, the metric score is assigned to NaN if an error occurs in estimator fitting and FitFailedWarning is raised." /> -->
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278 <!--fit_params-->
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279 <expand macro="pre_dispatch" />
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280 </section>
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281 </when>
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282 <when value="cross_val_predict">
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283 <section name="options" title="Other Options" expanded="false">
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284 <expand macro="model_validation_common_options" />
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285 <!--fit_params-->
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286 <expand macro="pre_dispatch" value="2*n_jobs’" help="Controls the number of jobs that get dispatched during parallel execution" />
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287 <param argument="method" type="select" label="Invokes the passed method name of the passed estimator">
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288 <option value="predict" selected="true">predict</option>
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289 <option value="predict_proba">predict_proba</option>
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290 </param>
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291 </section>
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292 </when>
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293 <when value="learning_curve">
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294 <section name="options" title="Other Options" expanded="false">
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295 <expand macro="scoring_selection" />
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296 <expand macro="model_validation_common_options" />
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297 <param argument="train_sizes" type="text" value="(0.1, 1.0, 5)" label="train_sizes"
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298 help="Relative or absolute numbers of training examples that will be used to generate the learning curve. Supports 1) tuple, to be evaled by np.linspace, e.g. (0.1, 1.0, 5); 2) array-like, e.g. [0.1 , 0.325, 0.55 , 0.775, 1.]">
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299 <sanitizer>
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300 <valid initial="default">
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301 <add value="[" />
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302 <add value="]" />
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303 </valid>
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304 </sanitizer>
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305 </param>
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306 <param argument="exploit_incremental_learning" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" help="Whether to apply incremental learning to speed up fitting of the estimator if supported" />
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307 <expand macro="pre_dispatch" />
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308 <expand macro="shuffle" checked="false" label="shuffle" help="Whether to shuffle training data before taking prefixes" />
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309 <expand macro="random_state" help_text="If int, the seed used by the random number generator. Used when `shuffle` is True" />
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310 </section>
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311 </when>
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312 <when value="permutation_test_score">
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313 <section name="options" title="Other Options" expanded="false">
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314 <expand macro="scoring_selection" />
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315 <expand macro="model_validation_common_options" />
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316 <param name="n_permutations" type="integer" value="100" optional="true" label="n_permutations" help="Number of times to permute y" />
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317 <expand macro="random_state" />
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318 </section>
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319 </when>
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320 <when value="validation_curve" />
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321 </conditional>
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322 <expand macro="sl_mixed_input_plus_sequence" />
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323 </inputs>
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324 <outputs>
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325 <data format="tabular" name="outfile" />
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326 </outputs>
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327 <tests>
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328 <test>
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329 <param name="infile_estimator" value="pipeline02" />
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330 <param name="selected_function" value="cross_validate" />
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331 <param name="return_train_score" value="True" />
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332 <param name="infile1" value="regression_train.tabular" ftype="tabular" />
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333 <param name="col1" value="1,2,3,4,5" />
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334 <param name="infile2" value="regression_train.tabular" ftype="tabular" />
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335 <param name="col2" value="6" />
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336 <output name="outfile">
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337 <assert_contents>
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338 <has_n_columns n="6" />
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339 <has_text text="0.9998136508657879" />
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340 <has_text text="0.9999980090366614" />
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341 <has_text text="0.9999977541353663" />
17
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342 </assert_contents>
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343 </output>
0
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344 </test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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345 <test>
28
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 24
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346 <param name="infile_estimator" value="pipeline02" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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347 <param name="selected_function" value="cross_val_predict" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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348 <param name="infile1" value="regression_train.tabular" ftype="tabular" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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349 <param name="col1" value="1,2,3,4,5" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 24
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350 <param name="infile2" value="regression_train.tabular" ftype="tabular" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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351 <param name="col2" value="6" />
34
1fe00785190d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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352 <output name="outfile">
1fe00785190d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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353 <assert_contents>
1fe00785190d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 30
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354 <has_n_columns n="1" />
1fe00785190d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 30
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355 <has_text text="1.5781414" />
1fe00785190d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 30
diff changeset
356 <has_text text="-1.19994559787" />
1fe00785190d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 30
diff changeset
357 <has_text text="-0.7187446" />
1fe00785190d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 30
diff changeset
358 <has_text text="0.324693926" />
1fe00785190d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 30
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359 <has_text text="1.25823227" />
1fe00785190d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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360 </assert_contents>
1fe00785190d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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361 </output>
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
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362 </test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
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363 <test>
28
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 24
diff changeset
364 <param name="infile_estimator" value="pipeline05" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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365 <param name="selected_function" value="learning_curve" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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366 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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367 <param name="header1" value="true" />
28
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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368 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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369 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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370 <param name="header2" value="true" />
28
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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371 <param name="col2" value="1" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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372 <output name="outfile" file="mv_result03.tabular" />
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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373 </test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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374 <test>
28
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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375 <param name="infile_estimator" value="pipeline05" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
376 <param name="selected_function" value="permutation_test_score" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
377 <param name="infile1" value="regression_train.tabular" ftype="tabular" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 24
diff changeset
378 <param name="col1" value="1,2,3,4,5" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
379 <param name="infile2" value="regression_train.tabular" ftype="tabular" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
380 <param name="col2" value="6" />
17
cf9aa11b91c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
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diff changeset
381 <output name="outfile">
cf9aa11b91c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
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382 <assert_contents>
28
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
383 <has_n_columns n="3" />
34
1fe00785190d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 30
diff changeset
384 <has_text text="-2.7453395018288753" />
17
cf9aa11b91c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents: 16
diff changeset
385 </assert_contents>
cf9aa11b91c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents: 16
diff changeset
386 </output>
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
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387 </test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
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388 <test>
28
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
389 <param name="infile_estimator" value="pipeline05" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
390 <param name="selected_function" value="cross_val_predict" />
17
cf9aa11b91c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
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diff changeset
391 <section name="groups_selector">
28
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
392 <param name="infile_groups" value="regression_y.tabular" ftype="tabular" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
393 <param name="header_g" value="true" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
394 <param name="selected_column_selector_option_g" value="by_index_number" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
395 <param name="col_g" value="1" />
17
cf9aa11b91c8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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diff changeset
396 </section>
28
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
397 <param name="selected_cv" value="GroupKFold" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 24
diff changeset
398 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 24
diff changeset
399 <param name="header1" value="true" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
400 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 24
diff changeset
401 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 24
diff changeset
402 <param name="header2" value="true" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 24
diff changeset
403 <param name="col2" value="1" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 24
diff changeset
404 <output name="outfile" file="mv_result05.tabular" />
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
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405 </test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
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406 </tests>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
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407 <help>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
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408 <![CDATA[
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
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409 **What it does**
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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410 This tool includes model validation functions to evaluate estimator performance in the cross-validation approach. This tool is based on
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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411 sklearn.model_selection package.
9
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
bgruening
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412 For information about model validation functions and their parameter settings please refer to `Scikit-learn model_selection`_.
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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diff changeset
413
9
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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414 .. _`Scikit-learn model_selection`: http://scikit-learn.org/stable/modules/classes.html#module-sklearn.model_selection
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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415 ]]>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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416 </help>
13
badd86b9ce24 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 12
diff changeset
417 <expand macro="sklearn_citation">
28
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 24
diff changeset
418 <expand macro="skrebate_citation" />
9b017b0da56e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
419 <expand macro="xgboost_citation" />
13
badd86b9ce24 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
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diff changeset
420 </expand>
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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421 </tool>