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annotate model_validation.xml @ 5:510aa2ce035e draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
author bgruening
date Sun, 01 Jul 2018 03:21:23 -0400
parents 60b8a683ba99
children fd7a054ffdbd
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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 json
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20 import pandas
2
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21 import ast
0
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22 import pickle
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23 import numpy as np
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24 import sklearn.model_selection
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25 from sklearn import svm, linear_model, ensemble
2
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26 from sklearn.pipeline import Pipeline
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27
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28 @COLUMNS_FUNCTION@
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29
2
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30 @FEATURE_SELECTOR_FUNCTION@
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31
0
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32 input_json_path = sys.argv[1]
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33 params = json.load(open(input_json_path, "r"))
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34
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35 input_type = params["input_options"]["selected_input"]
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36 if input_type=="tabular":
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37 header = 'infer' if params["input_options"]["header1"] else None
3
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38 column_option = params["input_options"]["column_selector_options_1"]["selected_column_selector_option"]
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39 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
3
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40 c = params["input_options"]["column_selector_options_1"]["col1"]
424d8d21744d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
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41 else:
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42 c = None
0
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43 X = read_columns(
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44 "$input_options.infile1",
3
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45 c = c,
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46 c_option = column_option,
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47 sep='\t',
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48 header=header,
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49 parse_dates=True
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50 )
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51 else:
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52 X = mmread(open("$input_options.infile1", 'r'))
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53
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54 header = 'infer' if params["input_options"]["header2"] else None
3
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55 column_option = params["input_options"]["column_selector_options_2"]["selected_column_selector_option2"]
5
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56 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
3
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57 c = params["input_options"]["column_selector_options_2"]["col2"]
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58 else:
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59 c = None
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60 y = read_columns(
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61 "$input_options.infile2",
3
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62 c = c,
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63 c_option = column_option,
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64 sep='\t',
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65 header=header,
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66 parse_dates=True
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67 )
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68 y=y.ravel()
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69
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70 options = params["model_validation_functions"]["options"]
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71 if 'scoring' in options and options['scoring'] == '':
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72 options['scoring'] = None
2
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73 if 'pre_dispatch' in options and options['pre_dispatch'] == '':
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74 options['pre_dispatch'] = None
0
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75
2
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76 pipeline_steps = []
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77
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78 ## Set up feature selector and add to pipeline steps.
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79 if params['feature_selection']['do_feature_selection'] == 'Yes':
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80 feature_selector = feature_selector(params['feature_selection']['feature_selection_algorithms'])
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81 pipeline_steps.append( ('feature_selector', feature_selector))
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82
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83 ## Set up estimator and add to pipeline.
0
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84 estimator=params["model_validation_functions"]["estimator"]
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85 if params["model_validation_functions"]["extra_estimator"]["has_estimator"] == 'no':
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86 estimator = params["model_validation_functions"]["extra_estimator"]["new_estimator"]
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87 estimator = eval(estimator.replace('__dq__', '"').replace("__sq__","'"))
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88
2
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89 pipeline_steps.append( ('estimator', estimator) )
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90
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91 pipeline = Pipeline(pipeline_steps)
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92
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93 ## Set up validator, run pipeline through validator and return results.
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94
2
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95 validator = params["model_validation_functions"]["selected_function"]
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96 validator = getattr(sklearn.model_selection, validator)
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97
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98 selected_function = params["model_validation_functions"]["selected_function"]
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99 rval_type = params["model_validation_functions"].get("return_type", None)
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100
2
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101 if selected_function == 'cross_validate':
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102 res = validator(pipeline, X, y, **options)
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103 rval = res[rval_type]
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104 elif selected_function == 'learning_curve':
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105 options['train_sizes'] = eval(options['train_sizes'])
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106 train_sizes_abs, train_scores, test_scores = validator(pipeline, X, y, **options)
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107 rval = eval(rval_type)
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108 elif selected_function == 'permutation_test_score':
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109 score, permutation_scores, pvalue = validator(pipeline, X, y, **options)
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110 rval = eval(rval_type)
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111 if rval_type in ["score", "pvalue"]:
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112 rval = [rval]
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113 elif selected_function == 'validation_curve':
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114 options['param_name'] = 'estimator__' + options['param_name']
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115 options['param_range'] = eval(options['param_range'])
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116 train_scores, test_scores = validator(pipeline, X, y, **options)
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117 rval = eval(rval_type)
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118 elif selected_function == 'GridSearchCV':
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119 param_grid = params["model_validation_functions"]["param_grid"].replace("__sq__","'")\
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120 .replace('__dq__','"').replace("__oc__", "{").replace("__cc__", "}")\
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121 .replace("__ob__", "[").replace("__cb__", "]")
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122 param_grid = ast.literal_eval(param_grid)
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123 grid = validator(pipeline, param_grid, **options)
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124 grid.fit(X, y)
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125 rval = getattr(grid, rval_type)
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126 if rval_type in ["best_estimator_", "best_score_", "best_index_"]:
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127 rval = [rval]
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128 else:
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129 rval = validator(pipeline, X, y, **options)
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130
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131 rval = pandas.DataFrame(rval)
2
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132 if rval_type and rval_type == "cv_results_":
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133 rval.to_csv(path_or_buf="$outfile", sep='\t', header=True, index=False)
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134 else:
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135 rval.to_csv(path_or_buf="$outfile", sep='\t', header=False, index=False)
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136
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137 ]]>
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138 </configfile>
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139 </configfiles>
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140 <inputs>
2
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141 <conditional name="feature_selection">
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142 <param name="do_feature_selection" type="select" label="Do feature selection?">
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143 <option value="No" selected="true"/>
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144 <option value="Yes"/>
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145 </param>
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146 <when value="No"/>
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147 <when value="Yes">
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148 <expand macro="feature_selection_all"/>
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149 </when>
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150 </conditional>
0
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151 <conditional name="model_validation_functions">
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152 <param name="selected_function" type="select" label="Select a model validation function">
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153 <option value="GridSearchCV">GridSearchCV - Exhaustive search over specified parameter values for an estimator </option>
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154 <option value="cross_validate">cross_validate - Evaluate metric(s) by cross-validation and also record fit/score times</option>
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155 <option value="cross_val_predict">cross_val_predict - Generate cross-validated estimates for each input data point</option>
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156 <option value="cross_val_score">cross_val_score - Evaluate a score by cross-validation</option>
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157 <option value="learning_curve">learning_curve - Learning curve</option>
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158 <option value="permutation_test_score">permutation_test_score - Evaluate the significance of a cross-validated score with permutations</option>
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159 <option value="validation_curve">validation_curve - Validation curve</option>
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160 </param>
2
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161 <when value="GridSearchCV">
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162 <expand macro="estimator_input_no_fit" />
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163 <param argument="param_grid" type="text" value="[{'feature_selector__k': [3, 5, 7, 9], 'estimator__C': [1, 10, 100, 1000]}]" label="param_grid" help="Dictionary with parameters names (string) as keys and lists of parameter settings to try as values, or a list of such dictionaries, in which case the grids spanned by each dictionary in the list are explored"/>
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164 <section name="options" title="Other Options" expanded="false">
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165 <expand macro="scoring"/>
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166 <expand macro="model_validation_common_options"/>
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167 <expand macro="pre_dispatch" value="2*n_jobs" help="Controls the number of jobs that get dispatched during parallel execution"/>
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168 <param argument="iid" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="iid" help="Data is identically distributed?"/>
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169 <param argument="refit" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="refit" help="Refit an estimator using the best found parameters on the whole dataset."/>
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170 <!--error_score-->
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171 <param argument="return_train_score" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="return_train_score" help=""/>
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172 </section>
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173 <param name="return_type" type="select" label="Select a return type">
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174 <option value="cv_results_" selected="true">cv_results_</option>
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175 <option value="best_estimator_">best_estimator_</option>
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176 <option value="best_score_">best_score_</option>
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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177 <option value="best_params_">best_params_</option>
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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178 <option value="best_index_">best_index_</option>
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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179 </param>
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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180 </when>
0
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181 <when value="cross_validate">
2
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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182 <expand macro="estimator_input_no_fit" />
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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183 <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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184 <!--groups-->
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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185 <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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186 <expand macro="scoring"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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187 <!--fit_params-->
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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188 <expand macro="pre_dispatch"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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189 </section>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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190 <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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191 <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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192 <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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193 <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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194 <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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195 </param>
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_predict">
2
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198 <expand macro="estimator_input_no_fit" />
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-->
2
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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201 <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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202 <!--fit_params-->
2
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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203 <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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204 <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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205 <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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206 <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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207 </param>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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208 </section>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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209 </when>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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210 <when value="cross_val_score">
2
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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211 <expand macro="estimator_input_no_fit" />
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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212 <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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213 <!--groups-->
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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214 <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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215 <expand macro="scoring"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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216 <!--fit_params-->
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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217 <expand macro="pre_dispatch"/>
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 </when>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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220 <when value="learning_curve">
2
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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221 <expand macro="estimator_input_no_fit" />
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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222 <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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223 <!--groups-->
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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224 <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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225 <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"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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226 <expand macro="scoring"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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227 <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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228 <expand macro="pre_dispatch"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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229 <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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230 <expand macro="random_state"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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231 </section>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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232 <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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233 <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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234 <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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235 <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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236 </param>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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237 </when>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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238 <when value="permutation_test_score">
2
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
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239 <expand macro="estimator_input_no_fit" />
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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240 <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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241 <!--groups-->
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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242 <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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243 <expand macro="scoring"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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244 <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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245 <expand macro="random_state"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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246 </section>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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247 <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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248 <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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249 <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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250 <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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251 </param>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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252 </when>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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253 <when value="validation_curve">
2
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254 <expand macro="estimator_input_no_fit" />
0
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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255 <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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256 <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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257 <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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258 <!--groups-->
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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259 <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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260 <expand macro="scoring"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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261 <expand macro="pre_dispatch"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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262 </section>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
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263 <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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diff changeset
264 <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
bgruening
parents:
diff changeset
265 <option value="test_scores">test_scores</option>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
266 </param>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
267 </when>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
268 </conditional>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
269 <expand macro="sl_mixed_input"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
270 </inputs>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
271 <outputs>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
272 <data format="tabular" name="outfile"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
273 </outputs>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
274 <tests>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
275 <test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
276 <param name="selected_function" value="cross_validate"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
277 <param name="estimator" value="linear_model.LassoCV()"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
278 <param name="has_estimator" value="yes"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
279 <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
bgruening
parents:
diff changeset
280 <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
bgruening
parents:
diff changeset
281 <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
bgruening
parents:
diff changeset
282 <param name="col2" value="6"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
283 <output name="outfile" file="mv_result01.tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
284 </test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
285 <test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
286 <param name="selected_function" value="cross_val_predict"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
287 <param name="estimator" value="linear_model.LassoCV()"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
288 <param name="has_estimator" value="yes"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
289 <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
bgruening
parents:
diff changeset
290 <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
bgruening
parents:
diff changeset
291 <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
bgruening
parents:
diff changeset
292 <param name="col2" value="6"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
293 <output name="outfile" file="mv_result02.tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
294 </test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
295 <test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
296 <param name="selected_function" value="cross_val_score"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
297 <param name="estimator" value="linear_model.LassoCV()"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
298 <param name="has_estimator" value="yes"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
299 <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
bgruening
parents:
diff changeset
300 <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
bgruening
parents:
diff changeset
301 <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
bgruening
parents:
diff changeset
302 <param name="col2" value="6"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
303 <output name="outfile" file="mv_result03.tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
304 </test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
305 <test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
306 <param name="selected_function" value="learning_curve"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
307 <param name="estimator" value="linear_model.LassoCV()"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
308 <param name="has_estimator" value="yes"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
309 <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
bgruening
parents:
diff changeset
310 <param name="header1" value="true" />
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
311 <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
bgruening
parents:
diff changeset
312 <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
bgruening
parents:
diff changeset
313 <param name="header2" value="true" />
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
314 <param name="col2" value="1"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
315 <output name="outfile" file="mv_result04.tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
316 </test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
317 <test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
318 <param name="selected_function" value="permutation_test_score"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
319 <param name="estimator" value="linear_model.LassoCV()"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
320 <param name="has_estimator" value="yes"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
321 <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
bgruening
parents:
diff changeset
322 <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
bgruening
parents:
diff changeset
323 <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
bgruening
parents:
diff changeset
324 <param name="col2" value="6"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
325 <output name="outfile" file="mv_result05.tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
326 </test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
327 <test>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
328 <param name="selected_function" value="validation_curve"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
329 <param name="estimator" value="svm.SVC(kernel=&quot;linear&quot;)"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
330 <param name="has_estimator" value="yes"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
331 <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
bgruening
parents:
diff changeset
332 <param name="header1" value="true" />
3
424d8d21744d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
bgruening
parents: 2
diff changeset
333 <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
bgruening
parents:
diff changeset
334 <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
bgruening
parents:
diff changeset
335 <param name="header2" value="true" />
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
336 <param name="col2" value="1"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
337 <param name="return_type" value="test_scores"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
338 <output name="outfile" file="mv_result06.tabular"/>
333507faecab planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2e1e78576b38110cf5b1f2ed83b08b9c3a6cbfee
bgruening
parents:
diff changeset
339 </test>
2
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 0
diff changeset
340 <test>
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 0
diff changeset
341 <param name="do_feature_selection" value="Yes"/>
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 0
diff changeset
342 <param name="selected_algorithm" value="SelectKBest"/>
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 0
diff changeset
343 <param name="score_func" value="chi2"/>
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 0
diff changeset
344 <param name="selected_function" value="GridSearchCV"/>
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 0
diff changeset
345 <param name="estimator" value="svm.SVR(kernel=&quot;linear&quot;)"/>
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 0
diff changeset
346 <param name="has_estimator" value="yes"/>
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 0
diff changeset
347 <param name="param_grid" value="[{'feature_selector__k': [3, 7], 'estimator__C': [1, 100]}]"/>
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 0
diff changeset
348 <param name="return_type" value="best_score_"/>
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 0
diff changeset
349 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
dd502cb0d567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
bgruening
parents: 0
diff changeset
350 <param name="header1" value="true" />
3
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351 <param name="selected_column_selector_option" value="all_columns"/>
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352 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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353 <param name="header2" value="true" />
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354 <param name="selected_column_selector_option2" value="all_columns"/>
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355 <output name="outfile" file="mv_result07.tabular"/>
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356 </test>
0
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357 </tests>
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358 <help>
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359 <![CDATA[
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360 **What it does**
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361 This tool includes model validation functions to evaluate estimator performance in the cross-validation approach. This tool is based on
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362 sklearn.model_selection package.
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363 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
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364
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365 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
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366 ]]>
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367 </help>
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368 <expand macro="sklearn_citation"/>
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369 </tool>