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annotate model_validation.xml @ 12:2c1851992069 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
author bgruening
date Fri, 17 Aug 2018 12:30:18 -0400
parents e4ab6b0bdf37
children badd86b9ce24
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1 <tool id="sklearn_model_validation" name="Model Validation" version="@VERSION@">
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2 <description>evaluates estimator performance by cross-validation</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 python "$sklearn_model_validation_script" '$inputs'
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12 ]]>
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13 </command>
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14 <configfiles>
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15 <inputs name="inputs" />
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16 <configfile name="sklearn_model_validation_script">
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17 <![CDATA[
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18 import sys
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19 import os
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20 import json
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21 import pandas
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22 import numpy as np
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23 from sklearn import preprocessing, model_selection, svm, linear_model, ensemble, naive_bayes, tree, neighbors
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24 from sklearn.pipeline import Pipeline
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26 execfile("$__tool_directory__/utils.py")
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28 safe_eval = SafeEval()
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29
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30 input_json_path = sys.argv[1]
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31 with open(input_json_path, "r") as param_handler:
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32 params = json.load(param_handler)
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33
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34 input_type = params["input_options"]["selected_input"]
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35 if input_type=="tabular":
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36 header = 'infer' if params["input_options"]["header1"] else None
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37 column_option = params["input_options"]["column_selector_options_1"]["selected_column_selector_option"]
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38 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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39 c = params["input_options"]["column_selector_options_1"]["col1"]
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40 else:
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41 c = None
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42 X = read_columns(
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43 "$input_options.infile1",
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44 c = c,
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45 c_option = column_option,
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46 sep='\t',
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47 header=header,
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48 parse_dates=True
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49 )
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50 else:
8
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51 X = mmread("$input_options.infile1")
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52
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53 header = 'infer' if params["input_options"]["header2"] else None
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54 column_option = params["input_options"]["column_selector_options_2"]["selected_column_selector_option2"]
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55 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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56 c = params["input_options"]["column_selector_options_2"]["col2"]
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57 else:
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58 c = None
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59 y = read_columns(
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60 "$input_options.infile2",
3
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61 c = c,
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62 c_option = column_option,
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63 sep='\t',
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64 header=header,
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65 parse_dates=True
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66 )
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67 y=y.ravel()
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68
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69 options = params["model_validation_functions"]["options"]
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70 options['cv'] = get_cv( options['cv'] )
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71 options['n_jobs'] = N_JOBS
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72 if 'scoring' in options:
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73 options['scoring'] = get_scoring(options['scoring'])
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74 if 'pre_dispatch' in options and options['pre_dispatch'] == '':
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75 options['pre_dispatch'] = None
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76
2
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77 pipeline_steps = []
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78
8
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79 ## Set up pre_processor and add to pipeline steps.
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80 if params['pre_processing']['do_pre_processing'] == 'Yes':
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81 preprocessor = params["pre_processing"]["pre_processors"]["selected_pre_processor"]
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82 pre_processor_options = params["pre_processing"]["pre_processors"]["options"]
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83 my_class = getattr(preprocessing, preprocessor)
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84 pipeline_steps.append( ('pre_processor', my_class(**pre_processor_options)) )
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85
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86 ## Set up feature selector and add to pipeline steps.
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87 if params['feature_selection']['do_feature_selection'] == 'Yes':
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88 feature_selector = feature_selector(params['feature_selection']['fs_algorithm_selector'])
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89 pipeline_steps.append( ('feature_selector', feature_selector) )
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90
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91 ## Set up estimator and add to pipeline.
9
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92 estimator_json = params["model_validation_functions"]['estimator_selector']
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93 estimator = get_estimator(estimator_json)
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94
2
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95 pipeline_steps.append( ('estimator', estimator) )
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96
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97 pipeline = Pipeline(pipeline_steps)
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98
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99 ## Set up validator, run pipeline through validator and return results.
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100
2
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101 validator = params["model_validation_functions"]["selected_function"]
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102 validator = getattr(model_selection, validator)
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103
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104 selected_function = params["model_validation_functions"]["selected_function"]
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105 rval_type = params["model_validation_functions"].get("return_type", None)
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106
2
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107 if selected_function == 'cross_validate':
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108 res = validator(pipeline, X, y, **options)
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109 rval = res[rval_type]
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110 elif selected_function == 'learning_curve':
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111 options['train_sizes'] = eval(options['train_sizes'])
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112 train_sizes_abs, train_scores, test_scores = validator(pipeline, X, y, **options)
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113 rval = eval(rval_type)
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114 elif selected_function == 'permutation_test_score':
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115 score, permutation_scores, pvalue = validator(pipeline, X, y, **options)
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116 rval = eval(rval_type)
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117 if rval_type in ["score", "pvalue"]:
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118 rval = [rval]
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119 elif selected_function == 'validation_curve':
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120 options['param_name'] = 'estimator__' + options['param_name']
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121 options['param_range'] = eval(options['param_range'])
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122 train_scores, test_scores = validator(pipeline, X, y, **options)
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123 rval = eval(rval_type)
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124 else:
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125 rval = validator(pipeline, X, y, **options)
0
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126
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127 rval = pandas.DataFrame(rval)
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128 rval.to_csv(path_or_buf="$outfile", sep='\t', header=False, index=False)
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129
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130 ]]>
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131 </configfile>
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132 </configfiles>
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133 <inputs>
8
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134 <conditional name="pre_processing">
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135 <param name="do_pre_processing" type="select" label="Do pre_processing?">
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136 <option value="No" selected="true"/>
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137 <option value="Yes"/>
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138 </param>
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139 <when value="No"/>
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140 <when value="Yes">
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141 <conditional name="pre_processors">
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142 <expand macro="sparse_preprocessors_ext" />
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143 <expand macro="sparse_preprocessor_options_ext" />
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144 </conditional>
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145 </when>
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146 </conditional>
2
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147 <conditional name="feature_selection">
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148 <param name="do_feature_selection" type="select" label="Do feature selection?">
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149 <option value="No" selected="true"/>
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150 <option value="Yes"/>
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151 </param>
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152 <when value="No"/>
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153 <when value="Yes">
9
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154 <expand macro="feature_selection_all">
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155 <expand macro="fs_selectfrommodel_no_prefitted"/>
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156 </expand>
2
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157 </when>
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158 </conditional>
0
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159 <conditional name="model_validation_functions">
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160 <param name="selected_function" type="select" label="Select a model validation function">
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161 <option value="cross_validate">cross_validate - Evaluate metric(s) by cross-validation and also record fit/score times</option>
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162 <option value="cross_val_predict">cross_val_predict - Generate cross-validated estimates for each input data point</option>
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163 <option value="cross_val_score">cross_val_score - Evaluate a score by cross-validation</option>
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164 <option value="learning_curve">learning_curve - Learning curve</option>
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165 <option value="permutation_test_score">permutation_test_score - Evaluate the significance of a cross-validated score with permutations</option>
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166 <option value="validation_curve">validation_curve - Validation curve</option>
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167 </param>
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168 <when value="cross_validate">
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169 <expand macro="estimator_selector_all" />
0
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170 <section name="options" title="Other Options" expanded="false">
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171 <!--groups-->
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172 <expand macro="model_validation_common_options"/>
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173 <expand macro="scoring_selection"/>
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174 <!--fit_params-->
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175 <expand macro="pre_dispatch"/>
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176 </section>
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177 <param name="return_type" type="select" label="Select a return type">
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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178 <option value="test_score" selected="true">test_score</option>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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179 <option value="train_score">train_score</option>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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180 <option value="fit_time">fit_time</option>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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181 <option value="score_time">score_time</option>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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182 </param>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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183 </when>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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184 <when value="cross_val_predict">
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185 <expand macro="estimator_selector_all" />
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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186 <section name="options" title="Other Options" expanded="false">
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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187 <!--groups-->
2
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188 <expand macro="model_validation_common_options" />
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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189 <!--fit_params-->
2
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190 <expand macro="pre_dispatch" value="2*n_jobs’" help="Controls the number of jobs that get dispatched during parallel execution"/>
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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191 <param argument="method" type="select" label="Invokes the passed method name of the passed estimator">
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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192 <option value="predict" selected="true">predict</option>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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193 <option value="predict_proba">predict_proba</option>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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194 </param>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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195 </section>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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196 </when>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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197 <when value="cross_val_score">
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c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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198 <expand macro="estimator_selector_all" />
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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199 <section name="options" title="Other Options" expanded="false">
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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200 <!--groups-->
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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201 <expand macro="model_validation_common_options"/>
12
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202 <expand macro="scoring_selection"/>
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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203 <!--fit_params-->
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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204 <expand macro="pre_dispatch"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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205 </section>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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206 </when>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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207 <when value="learning_curve">
9
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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208 <expand macro="estimator_selector_all" />
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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209 <section name="options" title="Other Options" expanded="false">
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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210 <!--groups-->
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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211 <expand macro="model_validation_common_options"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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212 <param argument="train_sizes" type="text" value="np.linspace(0.1, 1.0, 5)" label="train_sizes" help="Relative or absolute numbers of training examples that will be used to generate the learning curve"/>
12
2c1851992069 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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213 <expand macro="scoring_selection"/>
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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214 <param argument="exploit_incremental_learning" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="exploit_incremental_learning" help="Whether to apply incremental learning to speed up fitting of the estimator if supported"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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215 <expand macro="pre_dispatch"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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216 <expand macro="shuffle" checked="false" label="shuffle" help="Whether to shuffle training data before taking prefixes"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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217 <expand macro="random_state"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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218 </section>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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219 <param name="return_type" type="select" label="Select a return type">
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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220 <option value="train_sizes_abs" selected="true">train_sizes_abs</option>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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221 <option value="train_scores">train_scores</option>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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222 <option value="test_scores">test_scores</option>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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223 </param>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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224 </when>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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225 <when value="permutation_test_score">
9
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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226 <expand macro="estimator_selector_all" />
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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227 <section name="options" title="Other Options" expanded="false">
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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228 <!--groups-->
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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229 <expand macro="model_validation_common_options"/>
12
2c1851992069 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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diff changeset
230 <expand macro="scoring_selection"/>
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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231 <param name="n_permutations" type="integer" value="100" optional="true" label="n_permutations" help="Number of times to permute y"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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232 <expand macro="random_state"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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233 </section>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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234 <param name="return_type" type="select" label="Select a return type">
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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235 <option value="score" selected="true">score</option>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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236 <option value="permutation_scores">permutation_scores</option>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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237 <option value="pvalue">pvalue</option>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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238 </param>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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239 </when>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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240 <when value="validation_curve">
9
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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241 <expand macro="estimator_selector_all" />
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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242 <section name="options" title="Other Options" expanded="false">
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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243 <param name="param_name" type="text" value="gamma" label="param_name" help="Name of the parameter that will be varied"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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244 <param name="param_range" type="text" value="np.logspace(-6, -1, 5)" label="param_range" help="The values of the parameter that will be evaluated."/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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245 <!--groups-->
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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246 <expand macro="model_validation_common_options"/>
12
2c1851992069 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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diff changeset
247 <expand macro="scoring_selection"/>
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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248 <expand macro="pre_dispatch"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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249 </section>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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250 <param name="return_type" type="select" label="Select a return type">
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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251 <option value="train_scores" selected="true">train_scores</option>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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252 <option value="test_scores">test_scores</option>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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253 </param>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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254 </when>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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255 </conditional>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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256 <expand macro="sl_mixed_input"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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257 </inputs>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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258 <outputs>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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259 <data format="tabular" name="outfile"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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260 </outputs>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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261 <tests>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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262 <test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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263 <param name="selected_function" value="cross_validate"/>
9
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264 <param name="selected_module" value="linear_model"/>
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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265 <param name="selected_estimator" value="LassoCV"/>
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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266 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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267 <param name="col1" value="1,2,3,4,5"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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268 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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269 <param name="col2" value="6"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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270 <output name="outfile" file="mv_result01.tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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271 </test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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272 <test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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273 <param name="selected_function" value="cross_val_predict"/>
9
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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274 <param name="selected_module" value="linear_model"/>
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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275 <param name="selected_estimator" value="LassoCV"/>
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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276 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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277 <param name="col1" value="1,2,3,4,5"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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278 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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279 <param name="col2" value="6"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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280 <output name="outfile" file="mv_result02.tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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281 </test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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282 <test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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283 <param name="selected_function" value="cross_val_score"/>
9
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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284 <param name="selected_module" value="linear_model"/>
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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285 <param name="selected_estimator" value="LassoCV"/>
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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286 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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287 <param name="col1" value="1,2,3,4,5"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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288 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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289 <param name="col2" value="6"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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290 <output name="outfile" file="mv_result03.tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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291 </test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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292 <test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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293 <param name="selected_function" value="learning_curve"/>
9
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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294 <param name="selected_module" value="linear_model"/>
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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295 <param name="selected_estimator" value="LassoCV"/>
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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296 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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297 <param name="header1" value="true" />
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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298 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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299 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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300 <param name="header2" value="true" />
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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301 <param name="col2" value="1"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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302 <output name="outfile" file="mv_result04.tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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303 </test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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304 <test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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305 <param name="selected_function" value="permutation_test_score"/>
9
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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306 <param name="selected_module" value="linear_model"/>
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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307 <param name="selected_estimator" value="LassoCV"/>
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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308 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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309 <param name="col1" value="1,2,3,4,5"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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310 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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311 <param name="col2" value="6"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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312 <output name="outfile" file="mv_result05.tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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313 </test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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314 <test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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315 <param name="selected_function" value="validation_curve"/>
9
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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316 <param name="selected_module" value="svm"/>
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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317 <param name="selected_estimator" value="SVC"/>
12
2c1851992069 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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318 <param name="text_params" value="kernel='linear'"/>
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333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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319 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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320 <param name="header1" value="true" />
3
424d8d21744d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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321 <param name="selected_column_selector_option" value="all_columns"/>
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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322 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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323 <param name="header2" value="true" />
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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324 <param name="col2" value="1"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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325 <param name="return_type" value="test_scores"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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326 <output name="outfile" file="mv_result06.tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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327 </test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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328 </tests>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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329 <help>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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330 <![CDATA[
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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331 **What it does**
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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332 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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333 sklearn.model_selection package.
9
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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334 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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335
9
c6b3efcba7bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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336 .. _`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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337 ]]>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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338 </help>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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339 <expand macro="sklearn_citation"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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340 </tool>