Mercurial > repos > bgruening > sklearn_train_test_eval

comparison train_test_eval.xml @ 15:2eb5c017958d draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
author bgruening
date Wed, 09 Aug 2023 13:15:27 +0000
parents ead7adad8d0e
children
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14:4d1637cac794 15:2eb5c017958d
1 <tool id="sklearn_train_test_eval" name="Train, Test and Evaluation" version="@VERSION@" profile="20.05"> 1 <tool id="sklearn_train_test_eval" name="Train, Test and Evaluation" version="@VERSION@" profile="@PROFILE@">
2 <description>fit a model using part of dataset and evaluate using the rest</description> 2 <description>fit a model using part of dataset and evaluate using the rest</description>
3 <macros> 3 <macros>
4 <import>main_macros.xml</import> 4 <import>main_macros.xml</import>
5 <import>keras_macros.xml</import> 5 <import>keras_macros.xml</import>
6 </macros> 6 </macros>
83 <option value="save_weights">Model skeleton and weights, for deep learning exclusively</option> 83 <option value="save_weights">Model skeleton and weights, for deep learning exclusively</option>
84 </param> 84 </param>
85 </inputs> 85 </inputs>
86 <outputs> 86 <outputs>
87 <data format="tabular" name="outfile_result" /> 87 <data format="tabular" name="outfile_result" />
88 <data format="zip" name="outfile_object" label="Fitted estimator or estimator skeleton on ${on_string}"> 88 <data format="h5mlm" name="outfile_object" label="Fitted estimator or estimator skeleton on ${on_string}">
89 <filter>save != 'nope'</filter> 89 <filter>save != 'nope'</filter>
90 </data> 90 </data>
91 <data format="h5" name="outfile_weights" label="Weights trained on ${on_string}"> 91 <data format="h5" name="outfile_weights" label="Weights trained on ${on_string}">
92 <filter>save == 'save_weights'</filter> 92 <filter>save == 'save_weights'</filter>
93 </data> 93 </data>
94 </outputs> 94 </outputs>
95 <tests> 95 <tests>
96 <test> 96 <test>
97 <conditional name="experiment_schemes"> 97 <conditional name="experiment_schemes">
98 <param name="selected_exp_scheme" value="train_val_test" /> 98 <param name="selected_exp_scheme" value="train_val_test" />
99 <param name="infile_estimator" value="keras_model04" ftype="zip" /> 99 <param name="infile_estimator" value="keras_model04" ftype="h5mlm" />
100 <section name="hyperparams_swapping"> 100 <section name="hyperparams_swapping">
101 <param name="infile_params" value="keras_params04.tabular" ftype="tabular" /> 101 <param name="infile_params" value="keras_params04.tabular" ftype="tabular" />
102 <repeat name="param_set"> 102 <repeat name="param_set">
103 <param name="sp_value" value="999" /> 103 <param name="sp_value" value="999" />
104 <param name="sp_name" value="layers_0_Dense__config__kernel_initializer__config__seed" /> 104 <param name="sp_name" value="layers_1_Dense__config__kernel_initializer__config__seed" />
105 </repeat> 105 </repeat>
106 <repeat name="param_set"> 106 <repeat name="param_set">
107 <param name="sp_value" value="999" /> 107 <param name="sp_value" value="999" />
108 <param name="sp_name" value="layers_2_Dense__config__kernel_initializer__config__seed" /> 108 <param name="sp_name" value="layers_3_Dense__config__kernel_initializer__config__seed" />
109 </repeat> 109 </repeat>
110 <repeat name="param_set"> 110 <repeat name="param_set">
111 <param name="sp_value" value="0.1" /> 111 <param name="sp_value" value="0.1" />
112 <param name="sp_name" value="lr" /> 112 <param name="sp_name" value="learning_rate" />
113 </repeat> 113 </repeat>
114 <repeat name="param_set"> 114 <repeat name="param_set">
115 <param name="sp_value" value="'adamax'" /> 115 <param name="sp_value" value="'adamax'" />
116 <param name="sp_name" value="optimizer" /> 116 <param name="sp_name" value="optimizer" />
117 </repeat> 117 </repeat>
145 <param name="selected_column_selector_option2" value="all_columns" /> 145 <param name="selected_column_selector_option2" value="all_columns" />
146 <param name="save" value="save_weights" /> 146 <param name="save" value="save_weights" />
147 <output name="outfile_result"> 147 <output name="outfile_result">
148 <assert_contents> 148 <assert_contents>
149 <has_n_columns n="2" /> 149 <has_n_columns n="2" />
150 <has_text text="0.6384" />
151 <has_text text="-6.072" />
152 </assert_contents> 150 </assert_contents>
153 </output> 151 </output>
154 <output name="outfile_object" file="train_test_eval_model01" compare="sim_size" delta="5" />
155 <output name="outfile_weights" file="train_test_eval_weights01.h5" compare="sim_size" delta="5" /> 152 <output name="outfile_weights" file="train_test_eval_weights01.h5" compare="sim_size" delta="5" />
156 </test> 153 </test>
157 <test> 154 <test>
158 <conditional name="experiment_schemes"> 155 <conditional name="experiment_schemes">
159 <param name="selected_exp_scheme" value="train_val_test" /> 156 <param name="selected_exp_scheme" value="train_val_test" />
160 <param name="infile_estimator" value="keras_model04" ftype="zip" /> 157 <param name="infile_estimator" value="keras_model04" ftype="h5mlm" />
161 <section name="hyperparams_swapping"> 158 <section name="hyperparams_swapping">
162 <param name="infile_params" value="keras_params04.tabular" ftype="tabular" /> 159 <param name="infile_params" value="keras_params04.tabular" ftype="tabular" />
163 <repeat name="param_set"> 160 <repeat name="param_set">
164 <param name="sp_value" value="999" /> 161 <param name="sp_value" value="999" />
165 <param name="sp_name" value="layers_0_Dense__config__kernel_initializer__config__seed" /> 162 <param name="sp_name" value="layers_1_Dense__config__kernel_initializer__config__seed" />
166 </repeat> 163 </repeat>
167 <repeat name="param_set"> 164 <repeat name="param_set">
168 <param name="sp_value" value="999" /> 165 <param name="sp_value" value="999" />
169 <param name="sp_name" value="layers_2_Dense__config__kernel_initializer__config__seed" /> 166 <param name="sp_name" value="layers_3_Dense__config__kernel_initializer__config__seed" />
170 </repeat> 167 </repeat>
171 <repeat name="param_set"> 168 <repeat name="param_set">
172 <param name="sp_value" value="0.1" /> 169 <param name="sp_value" value="0.1" />
173 <param name="sp_name" value="lr" /> 170 <param name="sp_name" value="learning_rate" />
174 </repeat> 171 </repeat>
175 <repeat name="param_set"> 172 <repeat name="param_set">
176 <param name="sp_value" value="'adamax'" /> 173 <param name="sp_value" value="'adamax'" />
177 <param name="sp_name" value="optimizer" /> 174 <param name="sp_name" value="optimizer" />
178 </repeat> 175 </repeat>
212 <param name="selected_column_selector_option2" value="all_columns" /> 209 <param name="selected_column_selector_option2" value="all_columns" />
213 <param name="save" value="save_weights" /> 210 <param name="save" value="save_weights" />
214 <output name="outfile_result"> 211 <output name="outfile_result">
215 <assert_contents> 212 <assert_contents>
216 <has_n_columns n="2" /> 213 <has_n_columns n="2" />
217 <has_text text="0.627" />
218 <has_text text="-6.012" />
219 </assert_contents> 214 </assert_contents>
220 </output> 215 </output>
221 <output name="outfile_weights" file="train_test_eval_weights02.h5" compare="sim_size" delta="5" /> 216 <output name="outfile_weights" file="train_test_eval_weights02.h5" compare="sim_size" delta="5" />
222 </test> 217 </test>
223 <test> 218 <test>
224 <conditional name="experiment_schemes"> 219 <conditional name="experiment_schemes">
225 <param name="selected_exp_scheme" value="train_test" /> 220 <param name="selected_exp_scheme" value="train_test" />
226 <param name="infile_estimator" value="pipeline10" ftype="zip" /> 221 <param name="infile_estimator" value="pipeline10" ftype="h5mlm" />
227 <section name="hyperparams_swapping"> 222 <section name="hyperparams_swapping">
228 <param name="infile_params" value="get_params10.tabular" ftype="tabular" /> 223 <param name="infile_params" value="get_params10.tabular" ftype="tabular" />
229 <repeat name="param_set"> 224 <repeat name="param_set">
230 <param name="sp_value" value="10" /> 225 <param name="sp_value" value="10" />
231 <param name="sp_name" value="adaboostregressor__random_state" /> 226 <param name="sp_name" value="adaboostregressor__random_state" />
238 <section name="test_split"> 233 <section name="test_split">
239 <conditional name="split_algos"> 234 <conditional name="split_algos">
240 <param name="shuffle" value="simple" /> 235 <param name="shuffle" value="simple" />
241 <param name="test_size" value="0.2" /> 236 <param name="test_size" value="0.2" />
242 <param name="random_state" value="123" /> 237 <param name="random_state" value="123" />
243 </conditional>
244 </section>
245 <section name="val_split">
246 <conditional name="split_algos">
247 <param name="shuffle" value="simple" />
248 <param name="test_size" value="0.2" />
249 <param name="random_state" value="456" />
250 </conditional> 238 </conditional>
251 </section> 239 </section>
252 <section name="metrics"> 240 <section name="metrics">
253 <conditional name="scoring"> 241 <conditional name="scoring">
254 <param name="primary_scoring" value="r2" /> 242 <param name="primary_scoring" value="r2" />