Mercurial > repos > bgruening > sklearn_train_test_eval
diff train_test_eval.xml @ 9:ead7adad8d0e draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
| author | bgruening |
|---|---|
| date | Tue, 13 Apr 2021 18:45:35 +0000 |
| parents | 1b68acd5ac08 |
| children | 2eb5c017958d |
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--- a/train_test_eval.xml Fri Oct 02 08:43:15 2020 +0000 +++ b/train_test_eval.xml Tue Apr 13 18:45:35 2021 +0000 @@ -1,11 +1,11 @@ -<tool id="sklearn_train_test_eval" name="Train, Test and Evaluation" version="@VERSION@"> +<tool id="sklearn_train_test_eval" name="Train, Test and Evaluation" version="@VERSION@" profile="20.05"> <description>fit a model using part of dataset and evaluate using the rest</description> <macros> <import>main_macros.xml</import> <import>keras_macros.xml</import> </macros> - <expand macro="python_requirements"/> - <expand macro="macro_stdio"/> + <expand macro="python_requirements" /> + <expand macro="macro_stdio" /> <version_command>echo "@VERSION@"</version_command> <command detect_errors="aggressive"> <![CDATA[ @@ -51,32 +51,32 @@ <option value="train_val_test">Train, Validate and Test</option> </param> <when value="train_test"> - <expand macro="estimator_and_hyperparameter"/> + <expand macro="estimator_and_hyperparameter" /> <section name="test_split" title="Test holdout" expanded="false"> <expand macro="train_test_split_params"> - <expand macro="cv_groups"/> + <expand macro="cv_groups" /> </expand> </section> <section name="metrics" title="Metrics for evaluation" expanded="false"> - <expand macro="scoring_selection"/> + <expand macro="scoring_selection" /> </section> </when> <when value="train_val_test"> - <expand macro="estimator_and_hyperparameter"/> + <expand macro="estimator_and_hyperparameter" /> <section name="test_split" title="Test holdout" expanded="false"> <expand macro="train_test_split_params"> - <expand macro="cv_groups"/> + <expand macro="cv_groups" /> </expand> </section> <section name="val_split" title="Validation holdout (recommend using the same method for both validation and test)" expanded="false"> - <expand macro="train_test_split_params"/> + <expand macro="train_test_split_params" /> </section> <section name="metrics" title="Metrics for evaluation" expanded="false"> - <expand macro="scoring_selection"/> + <expand macro="scoring_selection" /> </section> </when> </conditional> - <expand macro="sl_mixed_input_plus_sequence"/> + <expand macro="sl_mixed_input_plus_sequence" /> <param name="save" type="select" label="Save the fitted model" help="For security reason, deep learning models will be saved into two datasets, model skeleton and weights."> <option value="nope" selected="true">Nope, save is unnecessary</option> <option value="save_estimator">Fitted whole estimator (excluding deep learning)</option> @@ -84,7 +84,7 @@ </param> </inputs> <outputs> - <data format="tabular" name="outfile_result"/> + <data format="tabular" name="outfile_result" /> <data format="zip" name="outfile_object" label="Fitted estimator or estimator skeleton on ${on_string}"> <filter>save != 'nope'</filter> </data> @@ -95,175 +95,175 @@ <tests> <test> <conditional name="experiment_schemes"> - <param name="selected_exp_scheme" value="train_val_test"/> - <param name="infile_estimator" value="keras_model04" ftype="zip"/> + <param name="selected_exp_scheme" value="train_val_test" /> + <param name="infile_estimator" value="keras_model04" ftype="zip" /> <section name="hyperparams_swapping"> - <param name="infile_params" value="keras_params04.tabular" ftype="tabular"/> + <param name="infile_params" value="keras_params04.tabular" ftype="tabular" /> <repeat name="param_set"> - <param name="sp_value" value="999"/> - <param name="sp_name" value="layers_0_Dense__config__kernel_initializer__config__seed"/> + <param name="sp_value" value="999" /> + <param name="sp_name" value="layers_0_Dense__config__kernel_initializer__config__seed" /> </repeat> <repeat name="param_set"> - <param name="sp_value" value="999"/> - <param name="sp_name" value="layers_2_Dense__config__kernel_initializer__config__seed"/> + <param name="sp_value" value="999" /> + <param name="sp_name" value="layers_2_Dense__config__kernel_initializer__config__seed" /> </repeat> <repeat name="param_set"> - <param name="sp_value" value="0.1"/> - <param name="sp_name" value="lr"/> + <param name="sp_value" value="0.1" /> + <param name="sp_name" value="lr" /> </repeat> <repeat name="param_set"> - <param name="sp_value" value="'adamax'"/> - <param name="sp_name" value="optimizer"/> + <param name="sp_value" value="'adamax'" /> + <param name="sp_name" value="optimizer" /> </repeat> </section> <section name="test_split"> <conditional name="split_algos"> - <param name="shuffle" value="simple"/> - <param name="test_size" value="0.2"/> - <param name="random_state" value="123"/> + <param name="shuffle" value="simple" /> + <param name="test_size" value="0.2" /> + <param name="random_state" value="123" /> </conditional> </section> <section name="val_split"> <conditional name="split_algos"> - <param name="shuffle" value="simple"/> - <param name="test_size" value="0.2"/> - <param name="random_state" value="456"/> + <param name="shuffle" value="simple" /> + <param name="test_size" value="0.2" /> + <param name="random_state" value="456" /> </conditional> </section> <section name="metrics"> <conditional name="scoring"> - <param name="primary_scoring" value="r2"/> - <param name="secondary_scoring" value="neg_mean_absolute_error"/> + <param name="primary_scoring" value="r2" /> + <param name="secondary_scoring" value="neg_mean_absolute_error" /> </conditional> </section> </conditional> - <param name="infile1" value="regression_X.tabular" ftype="tabular"/> + <param name="infile1" value="regression_X.tabular" ftype="tabular" /> <param name="header1" value="true" /> - <param name="selected_column_selector_option" value="all_columns"/> - <param name="infile2" value="regression_y.tabular" ftype="tabular"/> + <param name="selected_column_selector_option" value="all_columns" /> + <param name="infile2" value="regression_y.tabular" ftype="tabular" /> <param name="header2" value="true" /> - <param name="selected_column_selector_option2" value="all_columns"/> - <param name="save" value="save_weights"/> + <param name="selected_column_selector_option2" value="all_columns" /> + <param name="save" value="save_weights" /> <output name="outfile_result"> <assert_contents> - <has_n_columns n="2"/> - <has_text text="0.6626"/> - <has_text text="5.598"/> + <has_n_columns n="2" /> + <has_text text="0.6384" /> + <has_text text="-6.072" /> </assert_contents> </output> - <output name="outfile_object" file="train_test_eval_model01" compare="sim_size" delta="5"/> - <output name="outfile_weights" file="train_test_eval_weights01.h5" compare="sim_size" delta="5"/> + <output name="outfile_object" file="train_test_eval_model01" compare="sim_size" delta="5" /> + <output name="outfile_weights" file="train_test_eval_weights01.h5" compare="sim_size" delta="5" /> </test> <test> <conditional name="experiment_schemes"> - <param name="selected_exp_scheme" value="train_val_test"/> - <param name="infile_estimator" value="keras_model04" ftype="zip"/> + <param name="selected_exp_scheme" value="train_val_test" /> + <param name="infile_estimator" value="keras_model04" ftype="zip" /> <section name="hyperparams_swapping"> - <param name="infile_params" value="keras_params04.tabular" ftype="tabular"/> + <param name="infile_params" value="keras_params04.tabular" ftype="tabular" /> <repeat name="param_set"> - <param name="sp_value" value="999"/> - <param name="sp_name" value="layers_0_Dense__config__kernel_initializer__config__seed"/> + <param name="sp_value" value="999" /> + <param name="sp_name" value="layers_0_Dense__config__kernel_initializer__config__seed" /> </repeat> <repeat name="param_set"> - <param name="sp_value" value="999"/> - <param name="sp_name" value="layers_2_Dense__config__kernel_initializer__config__seed"/> + <param name="sp_value" value="999" /> + <param name="sp_name" value="layers_2_Dense__config__kernel_initializer__config__seed" /> </repeat> <repeat name="param_set"> - <param name="sp_value" value="0.1"/> - <param name="sp_name" value="lr"/> + <param name="sp_value" value="0.1" /> + <param name="sp_name" value="lr" /> </repeat> <repeat name="param_set"> - <param name="sp_value" value="'adamax'"/> - <param name="sp_name" value="optimizer"/> + <param name="sp_value" value="'adamax'" /> + <param name="sp_name" value="optimizer" /> </repeat> </section> <section name="test_split"> <conditional name="split_algos"> - <param name="shuffle" value="group"/> - <param name="group_names" value="test"/> + <param name="shuffle" value="group" /> + <param name="group_names" value="test" /> <section name="groups_selector"> - <param name="infile_g" value="regression_groups.tabular" ftype="tabular"/> - <param name="header_g" value="true"/> + <param name="infile_g" value="regression_groups.tabular" ftype="tabular" /> + <param name="header_g" value="true" /> <conditional name="column_selector_options_g"> - <param name="selected_column_selector_option_g" value="by_index_number"/> - <param name="col_g" value="1"/> + <param name="selected_column_selector_option_g" value="by_index_number" /> + <param name="col_g" value="1" /> </conditional> </section> </conditional> </section> <section name="val_split"> <conditional name="split_algos"> - <param name="shuffle" value="group"/> - <param name="group_names" value="validation"/> + <param name="shuffle" value="group" /> + <param name="group_names" value="validation" /> </conditional> </section> <section name="metrics"> <conditional name="scoring"> - <param name="primary_scoring" value="r2"/> - <param name="secondary_scoring" value="neg_mean_absolute_error"/> + <param name="primary_scoring" value="r2" /> + <param name="secondary_scoring" value="neg_mean_absolute_error" /> </conditional> </section> </conditional> - <param name="infile1" value="regression_X.tabular" ftype="tabular"/> + <param name="infile1" value="regression_X.tabular" ftype="tabular" /> <param name="header1" value="true" /> - <param name="selected_column_selector_option" value="all_columns"/> - <param name="infile2" value="regression_y.tabular" ftype="tabular"/> + <param name="selected_column_selector_option" value="all_columns" /> + <param name="infile2" value="regression_y.tabular" ftype="tabular" /> <param name="header2" value="true" /> - <param name="selected_column_selector_option2" value="all_columns"/> - <param name="save" value="save_weights"/> - <output name="outfile_result" > + <param name="selected_column_selector_option2" value="all_columns" /> + <param name="save" value="save_weights" /> + <output name="outfile_result"> <assert_contents> - <has_n_columns n="2"/> - <has_text text="0.667"/> - <has_text text="-5.586"/> + <has_n_columns n="2" /> + <has_text text="0.627" /> + <has_text text="-6.012" /> </assert_contents> </output> - <output name="outfile_weights" file="train_test_eval_weights02.h5" compare="sim_size" delta="5"/> + <output name="outfile_weights" file="train_test_eval_weights02.h5" compare="sim_size" delta="5" /> </test> <test> <conditional name="experiment_schemes"> - <param name="selected_exp_scheme" value="train_test"/> - <param name="infile_estimator" value="pipeline10" ftype="zip"/> + <param name="selected_exp_scheme" value="train_test" /> + <param name="infile_estimator" value="pipeline10" ftype="zip" /> <section name="hyperparams_swapping"> - <param name="infile_params" value="get_params10.tabular" ftype="tabular"/> + <param name="infile_params" value="get_params10.tabular" ftype="tabular" /> <repeat name="param_set"> - <param name="sp_value" value="10"/> - <param name="sp_name" value="adaboostregressor__random_state"/> + <param name="sp_value" value="10" /> + <param name="sp_name" value="adaboostregressor__random_state" /> </repeat> <repeat name="param_set"> - <param name="sp_value" value=": sklearn_tree.ExtraTreeRegressor(random_state=0)"/> - <param name="sp_name" value="adaboostregressor__base_estimator"/> + <param name="sp_value" value=": sklearn_tree.ExtraTreeRegressor(random_state=0)" /> + <param name="sp_name" value="adaboostregressor__base_estimator" /> </repeat> </section> <section name="test_split"> <conditional name="split_algos"> - <param name="shuffle" value="simple"/> - <param name="test_size" value="0.2"/> - <param name="random_state" value="123"/> + <param name="shuffle" value="simple" /> + <param name="test_size" value="0.2" /> + <param name="random_state" value="123" /> </conditional> </section> <section name="val_split"> <conditional name="split_algos"> - <param name="shuffle" value="simple"/> - <param name="test_size" value="0.2"/> - <param name="random_state" value="456"/> + <param name="shuffle" value="simple" /> + <param name="test_size" value="0.2" /> + <param name="random_state" value="456" /> </conditional> </section> <section name="metrics"> <conditional name="scoring"> - <param name="primary_scoring" value="r2"/> - <param name="secondary_scoring" value="neg_mean_absolute_error"/> + <param name="primary_scoring" value="r2" /> + <param name="secondary_scoring" value="neg_mean_absolute_error" /> </conditional> </section> </conditional> - <param name="infile1" value="regression_X.tabular" ftype="tabular"/> + <param name="infile1" value="regression_X.tabular" ftype="tabular" /> <param name="header1" value="true" /> - <param name="selected_column_selector_option" value="all_columns"/> - <param name="infile2" value="regression_y.tabular" ftype="tabular"/> + <param name="selected_column_selector_option" value="all_columns" /> + <param name="infile2" value="regression_y.tabular" ftype="tabular" /> <param name="header2" value="true" /> - <param name="selected_column_selector_option2" value="all_columns"/> - <param name="save" value="nope"/> - <output name="outfile_result" file="train_test_eval03.tabular"/> + <param name="selected_column_selector_option2" value="all_columns" /> + <param name="save" value="nope" /> + <output name="outfile_result" file="train_test_eval03.tabular" /> </test> </tests> <help> @@ -283,8 +283,8 @@ ]]> </help> <expand macro="sklearn_citation"> - <expand macro="skrebate_citation"/> - <expand macro="xgboost_citation"/> - <expand macro="keras_citation"/> + <expand macro="skrebate_citation" /> + <expand macro="xgboost_citation" /> + <expand macro="keras_citation" /> </expand> </tool>