Mercurial > repos > bgruening > sklearn_train_test_eval
comparison train_test_eval.xml @ 15:2eb5c017958d draft
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 |
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| 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" /> |