Mercurial > repos > bgruening > sklearn_model_validation
diff model_validation.xml @ 28:9b017b0da56e draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
author | bgruening |
---|---|
date | Tue, 13 Apr 2021 19:01:30 +0000 |
parents | a5aed87b2cc0 |
children | 4b359039f09f |
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--- a/model_validation.xml Fri Oct 02 08:51:25 2020 +0000 +++ b/model_validation.xml Tue Apr 13 19:01:30 2021 +0000 @@ -1,10 +1,10 @@ -<tool id="sklearn_model_validation" name="Model Validation" version="@VERSION@"> +<tool id="sklearn_model_validation" name="Model Validation" version="@VERSION@" profile="20.05"> <description>includes cross_validate, cross_val_predict, learning_curve, and more</description> <macros> <import>main_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> <![CDATA[ @@ -267,7 +267,7 @@ </configfile> </configfiles> <inputs> - <param name="infile_estimator" type="data" format="zip" label="Choose the dataset containing model/pipeline object"/> + <param name="infile_estimator" type="data" format="zip" label="Choose the dataset containing model/pipeline object" /> <conditional name="model_validation_functions"> <param name="selected_function" type="select" label="Select a model validation function"> <option value="cross_validate">cross_validate - Evaluate metric(s) by cross-validation and also record fit/score times</option> @@ -278,20 +278,20 @@ </param> <when value="cross_validate"> <section name="options" title="Other Options" expanded="false"> - <expand macro="scoring_selection"/> - <expand macro="model_validation_common_options"/> - <param argument="return_train_score" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" help="Whether to include train scores."/> + <expand macro="scoring_selection" /> + <expand macro="model_validation_common_options" /> + <param argument="return_train_score" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" help="Whether to include train scores." /> <!--param argument="return_estimator" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" help="Whether to return the estimators fitted on each split."/> --> <!--param argument="error_score" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Raise fit error:" help="If false, the metric score is assigned to NaN if an error occurs in estimator fitting and FitFailedWarning is raised."/> --> <!--fit_params--> - <expand macro="pre_dispatch"/> + <expand macro="pre_dispatch" /> </section> </when> <when value="cross_val_predict"> <section name="options" title="Other Options" expanded="false"> <expand macro="model_validation_common_options" /> <!--fit_params--> - <expand macro="pre_dispatch" value="2*n_jobs’" help="Controls the number of jobs that get dispatched during parallel execution"/> + <expand macro="pre_dispatch" value="2*n_jobs’" help="Controls the number of jobs that get dispatched during parallel execution" /> <param argument="method" type="select" label="Invokes the passed method name of the passed estimator"> <option value="predict" selected="true">predict</option> <option value="predict_proba">predict_proba</option> @@ -300,107 +300,106 @@ </when> <when value="learning_curve"> <section name="options" title="Other Options" expanded="false"> - <expand macro="scoring_selection"/> - <expand macro="model_validation_common_options"/> - <param argument="train_sizes" type="text" value="(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. Supports 1) tuple, to be evaled by np.linspace, e.g. (0.1, 1.0, 5); 2) array-like, e.g. [0.1 , 0.325, 0.55 , 0.775, 1.]"> + <expand macro="scoring_selection" /> + <expand macro="model_validation_common_options" /> + <param argument="train_sizes" type="text" value="(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. Supports 1) tuple, to be evaled by np.linspace, e.g. (0.1, 1.0, 5); 2) array-like, e.g. [0.1 , 0.325, 0.55 , 0.775, 1.]"> <sanitizer> <valid initial="default"> - <add value="["/> - <add value="]"/> + <add value="[" /> + <add value="]" /> </valid> </sanitizer> </param> - <param argument="exploit_incremental_learning" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" help="Whether to apply incremental learning to speed up fitting of the estimator if supported"/> - <expand macro="pre_dispatch"/> - <expand macro="shuffle" checked="false" label="shuffle" help="Whether to shuffle training data before taking prefixes"/> - <expand macro="random_state" help_text="If int, the seed used by the random number generator. Used when `shuffle` is True"/> + <param argument="exploit_incremental_learning" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" help="Whether to apply incremental learning to speed up fitting of the estimator if supported" /> + <expand macro="pre_dispatch" /> + <expand macro="shuffle" checked="false" label="shuffle" help="Whether to shuffle training data before taking prefixes" /> + <expand macro="random_state" help_text="If int, the seed used by the random number generator. Used when `shuffle` is True" /> </section> </when> <when value="permutation_test_score"> <section name="options" title="Other Options" expanded="false"> - <expand macro="scoring_selection"/> - <expand macro="model_validation_common_options"/> - <param name="n_permutations" type="integer" value="100" optional="true" label="n_permutations" help="Number of times to permute y"/> - <expand macro="random_state"/> + <expand macro="scoring_selection" /> + <expand macro="model_validation_common_options" /> + <param name="n_permutations" type="integer" value="100" optional="true" label="n_permutations" help="Number of times to permute y" /> + <expand macro="random_state" /> </section> </when> - <when value="validation_curve"/> + <when value="validation_curve" /> </conditional> - <expand macro="sl_mixed_input_plus_sequence"/> + <expand macro="sl_mixed_input_plus_sequence" /> </inputs> <outputs> - <data format="tabular" name="outfile"/> + <data format="tabular" name="outfile" /> </outputs> <tests> <test> - <param name="infile_estimator" value="pipeline02"/> - <param name="selected_function" value="cross_validate"/> - <param name="return_train_score" value="True"/> - <param name="infile1" value="regression_train.tabular" ftype="tabular"/> - <param name="col1" value="1,2,3,4,5"/> - <param name="infile2" value="regression_train.tabular" ftype="tabular"/> - <param name="col2" value="6"/> + <param name="infile_estimator" value="pipeline02" /> + <param name="selected_function" value="cross_validate" /> + <param name="return_train_score" value="True" /> + <param name="infile1" value="regression_train.tabular" ftype="tabular" /> + <param name="col1" value="1,2,3,4,5" /> + <param name="infile2" value="regression_train.tabular" ftype="tabular" /> + <param name="col2" value="6" /> <output name="outfile"> <assert_contents> - <has_n_columns n="6"/> - <has_text text="0.9999961390418067"/> - <has_text text="0.9944541531269271"/> - <has_text text="0.9999193322454393"/> + <has_n_columns n="6" /> + <has_text text="0.9999961390418067" /> + <has_text text="0.9944541531269271" /> + <has_text text="0.9999193322454393" /> </assert_contents> </output> </test> <test> - <param name="infile_estimator" value="pipeline02"/> - <param name="selected_function" value="cross_val_predict"/> - <param name="infile1" value="regression_train.tabular" ftype="tabular"/> - <param name="col1" value="1,2,3,4,5"/> - <param name="infile2" value="regression_train.tabular" ftype="tabular"/> - <param name="col2" value="6"/> - <output name="outfile" file="mv_result02.tabular" lines_diff="14"/> + <param name="infile_estimator" value="pipeline02" /> + <param name="selected_function" value="cross_val_predict" /> + <param name="infile1" value="regression_train.tabular" ftype="tabular" /> + <param name="col1" value="1,2,3,4,5" /> + <param name="infile2" value="regression_train.tabular" ftype="tabular" /> + <param name="col2" value="6" /> + <output name="outfile" file="mv_result02.tabular" lines_diff="14" /> </test> <test> - <param name="infile_estimator" value="pipeline05"/> - <param name="selected_function" value="learning_curve"/> - <param name="infile1" value="regression_X.tabular" ftype="tabular"/> + <param name="infile_estimator" value="pipeline05" /> + <param name="selected_function" value="learning_curve" /> + <param name="infile1" value="regression_X.tabular" ftype="tabular" /> <param name="header1" value="true" /> - <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/> - <param name="infile2" value="regression_y.tabular" ftype="tabular"/> + <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" /> + <param name="infile2" value="regression_y.tabular" ftype="tabular" /> <param name="header2" value="true" /> - <param name="col2" value="1"/> - <output name="outfile" file="mv_result03.tabular"/> + <param name="col2" value="1" /> + <output name="outfile" file="mv_result03.tabular" /> </test> <test> - <param name="infile_estimator" value="pipeline05"/> - <param name="selected_function" value="permutation_test_score"/> - <param name="infile1" value="regression_train.tabular" ftype="tabular"/> - <param name="col1" value="1,2,3,4,5"/> - <param name="infile2" value="regression_train.tabular" ftype="tabular"/> - <param name="col2" value="6"/> + <param name="infile_estimator" value="pipeline05" /> + <param name="selected_function" value="permutation_test_score" /> + <param name="infile1" value="regression_train.tabular" ftype="tabular" /> + <param name="col1" value="1,2,3,4,5" /> + <param name="infile2" value="regression_train.tabular" ftype="tabular" /> + <param name="col2" value="6" /> <output name="outfile"> <assert_contents> - <has_n_columns n="3"/> - <has_text text="0.25697059258228816"/> + <has_n_columns n="3" /> + <has_text text="0.25697059258228816" /> </assert_contents> </output> </test> <test> - <param name="infile_estimator" value="pipeline05"/> - <param name="selected_function" value="cross_val_predict"/> + <param name="infile_estimator" value="pipeline05" /> + <param name="selected_function" value="cross_val_predict" /> <section name="groups_selector"> - <param name="infile_groups" value="regression_y.tabular" ftype="tabular"/> - <param name="header_g" value="true"/> - <param name="selected_column_selector_option_g" value="by_index_number"/> - <param name="col_g" value="1"/> + <param name="infile_groups" value="regression_y.tabular" ftype="tabular" /> + <param name="header_g" value="true" /> + <param name="selected_column_selector_option_g" value="by_index_number" /> + <param name="col_g" value="1" /> </section> - <param name="selected_cv" value="GroupKFold"/> - <param name="infile1" value="regression_X.tabular" ftype="tabular"/> - <param name="header1" value="true"/> - <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/> - <param name="infile2" value="regression_y.tabular" ftype="tabular"/> - <param name="header2" value="true"/> - <param name="col2" value="1"/> - <output name="outfile" file="mv_result05.tabular"/> + <param name="selected_cv" value="GroupKFold" /> + <param name="infile1" value="regression_X.tabular" ftype="tabular" /> + <param name="header1" value="true" /> + <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" /> + <param name="infile2" value="regression_y.tabular" ftype="tabular" /> + <param name="header2" value="true" /> + <param name="col2" value="1" /> + <output name="outfile" file="mv_result05.tabular" /> </test> </tests> <help> @@ -414,7 +413,7 @@ ]]> </help> <expand macro="sklearn_citation"> - <expand macro="skrebate_citation"/> - <expand macro="xgboost_citation"/> + <expand macro="skrebate_citation" /> + <expand macro="xgboost_citation" /> </expand> </tool>