comparison keras_train_and_eval.xml @ 4:3866911c93ae draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"

3:f1b9a42d6809

<tool id="keras_train_and_eval" name="Deep learning training and evaluation" version="@VERSION@">
    <description>conduct deep training and evaluation either implicitly or explicitly</description>
    <macros>
        <import>main_macros.xml</import>
        <import>keras_macros.xml</import>
    </macros>
    <expand macro="python_requirements"/>
    <expand macro="macro_stdio"/>
    <version_command>echo "@VERSION@"</version_command>
    <command>
        <![CDATA[
        export HDF5_USE_FILE_LOCKING='FALSE';
        #if $input_options.selected_input == 'refseq_and_interval'

        #end if
        python '$__tool_directory__/keras_train_and_eval.py'
            --inputs '$inputs'
            --estimator '$experiment_schemes.infile_estimator'
            #if $input_options.selected_input == 'seq_fasta'
            --fasta_path '$input_options.fasta_path'
            #elif $input_options.selected_input == 'refseq_and_interval'
            --ref_seq "`pwd`/${ref_genome_file.element_identifier}"
            --interval '$input_options.interval_file'
            --targets "`pwd`/${target_file.element_identifier}.gz"
            #else
            --infile1 '$input_options.infile1'
            #end if
            --infile2 '$input_options.infile2'
            --outfile_result "`pwd`/tmp_outfile_result"
            #if $save and 'save_estimator' in str($save)
            --outfile_object '$outfile_object'
            --outfile_weights '$outfile_weights'
            #end if
            #if $save and 'save_prediction' in str($save)
            --outfile_y_true '$outfile_y_true'
            --outfile_y_preds '$outfile_y_preds'
            #end if
            #if $experiment_schemes.test_split.split_algos.shuffle == 'group'
            --groups '$experiment_schemes.test_split.split_algos.groups_selector.infile_g'
            #end if
            >'$outfile_result' && cp '$outfile_result' "`pwd`/../tool_stdout"
            && cp tmp_outfile_result '$outfile_result';

        ]]>
    </command>
    <configfiles>
        <inputs name="inputs" />
    </configfiles>

            <param name="selected_exp_scheme" type="select" label="Select a scheme">
                <option value="train_val" selected="true">Train and Validate</option>
                <option value="train_val_test">Train, Validate and and Evaluate</option>
            </param>
            <when value="train_val">
                <expand macro="estimator_and_hyperparameter"/>
                <section name="test_split" title="Validation holdout" expanded="false">
                    <expand macro="train_test_split_params">
                        <expand macro="cv_groups"/>
                    </expand>
                </section>
                <section name="metrics" title="Metrics for evaluation" expanded="false">
                    <expand macro="scoring_selection"/>
                </section>
            </when>
            <when value="train_val_test">
                <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>
                </section>
                <section name="val_split" title="Validation holdout (recommend using the same splitting method as for test holdout)" expanded="false">
                    <expand macro="train_test_split_params"/>
                </section>
                <section name="metrics" title="Metrics for evaluation" expanded="false">
                    <expand macro="scoring_selection"/>
                </section>
            </when>
        </conditional>
        <expand macro="sl_mixed_input_plus_sequence"/>
        <param name="save" type="select" multiple='true' display="checkboxes" label="Save the fitted model" optional="true" help="Evaluation scores will be output by default.">
            <option value="save_estimator" selected="true">Fitted estimator in skeleton and weights, separately</option>
            <option value="save_prediction">True labels and prediction results from evaluation for downstream analysis</option>
        </param>
    </inputs>
    <outputs>
        <data format="tabular" name="outfile_result"/>
        <data format="zip" name="outfile_object" label="Fitted estimator or estimator skeleton on ${on_string}">
            <filter>str(save) and 'save_estimator' in str(save)</filter>
        </data>
        <data format="h5" name="outfile_weights" label="Weights trained on ${on_string}">
            <filter>str(save) and 'save_estimator' in str(save)</filter>

        </data>
    </outputs>
    <tests>
        <test>
            <conditional name="experiment_schemes">
                <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"/>
                    <repeat name="param_set">
                        <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"/>
                    </repeat>
                    <repeat name="param_set">
                        <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"/>
                    </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"/>
                    </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"/>
                    </conditional>
                </section>
                <section name="metrics">
                    <conditional name="scoring">
                        <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="header1" value="true" />
            <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_estimator"/>
            <output name="outfile_result">
                <assert_contents>
                    <has_n_columns n="2"/>
                    <has_text text="0.6626"/>
                    <has_text text="5.598"/>
                </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"/>
        </test>
        <test>
            <conditional name="experiment_schemes">
                <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"/>
                    <repeat name="param_set">
                        <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"/>
                    </repeat>
                    <repeat name="param_set">
                        <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"/>
                    </repeat>
                </section>
                <section name="test_split">
                    <conditional name="split_algos">
                        <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"/>
                            <conditional name="column_selector_options_g">
                                <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"/>
                    </conditional>
                </section>
                <section name="metrics">
                    <conditional name="scoring">
                        <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="header1" value="true" />
            <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_estimator,save_prediction"/>
            <output name="outfile_result" >
                <assert_contents>
                    <has_n_columns n="2"/>
                    <has_text text="0.667"/>
                    <has_text text="5.586"/>
                </assert_contents>
            </output>
            <output name="outfile_weights" file="train_test_eval_weights02.h5" compare="sim_size" delta="5"/>
            <output name="outfile_y_true" file="keras_train_eval_y_true02.tabular" ftype="tabular"/>
        </test>
        <test>
            <conditional name="experiment_schemes">
                <param name="selected_exp_scheme" value="train_val"/>
                <param name="infile_estimator" value="pipeline10" ftype="zip"/>
                <section name="hyperparams_swapping">
                    <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"/>
                    </repeat>
                    <repeat name="param_set">
                        <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"/>
                    </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"/>
                    </conditional>
                </section>
                <section name="metrics">
                    <conditional name="scoring">
                        <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="header1" value="true" />
            <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=""/>
            <output name="outfile_result" file="train_test_eval03.tabular"/>
        </test>
    </tests>
    <help>
        <![CDATA[
**What it does**

- true labels or values and predicted values from the evaluation

        ]]>
    </help>
    <expand macro="sklearn_citation">
        <expand macro="keras_citation"/>
    </expand>
</tool>

4:3866911c93ae

<tool id="keras_train_and_eval" name="Deep learning training and evaluation" version="@VERSION@" profile="20.05">
    <description>conduct deep training and evaluation either implicitly or explicitly</description>
    <macros>
        <import>main_macros.xml</import>
        <import>keras_macros.xml</import>
    </macros>
    <expand macro="python_requirements" />
    <expand macro="macro_stdio" />
    <version_command>echo "@VERSION@"</version_command>
    <command>
        <![CDATA[
        export HDF5_USE_FILE_LOCKING='FALSE';
        #if $input_options.selected_input == 'refseq_and_interval'

        #end if
        python '$__tool_directory__/keras_train_and_eval.py'
            --inputs '$inputs'
            --estimator '$experiment_schemes.infile_estimator'
            #if $input_options.selected_input == 'seq_fasta'
                --fasta_path '$input_options.fasta_path'
            #elif $input_options.selected_input == 'refseq_and_interval'
                --ref_seq "`pwd`/${ref_genome_file.element_identifier}"
                --interval '$input_options.interval_file'
                --targets "`pwd`/${target_file.element_identifier}.gz"
            #else
                --infile1 '$input_options.infile1'
            #end if
                --infile2 '$input_options.infile2'
                --outfile_result '$outfile_result'
            #if $save and 'save_estimator' in str($save)
                --outfile_object '$outfile_object'
                --outfile_weights '$outfile_weights'
            #end if
            #if $save and 'save_prediction' in str($save)
                --outfile_y_true '$outfile_y_true'
                --outfile_y_preds '$outfile_y_preds'
            #end if
            #if $experiment_schemes.test_split.split_algos.shuffle == 'group'
                --groups '$experiment_schemes.test_split.split_algos.groups_selector.infile_g'
            #end if
        ]]>
    </command>
    <configfiles>
        <inputs name="inputs" />
    </configfiles>

            <param name="selected_exp_scheme" type="select" label="Select a scheme">
                <option value="train_val" selected="true">Train and Validate</option>
                <option value="train_val_test">Train, Validate and and Evaluate</option>
            </param>
            <when value="train_val">
                <expand macro="estimator_and_hyperparameter" />
                <section name="test_split" title="Validation holdout" expanded="false">
                    <expand macro="train_test_split_params">
                        <expand macro="cv_groups" />
                    </expand>
                </section>
                <section name="metrics" title="Metrics for evaluation" expanded="false">
                    <expand macro="scoring_selection" />
                </section>
            </when>
            <when value="train_val_test">
                <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>
                </section>
                <section name="val_split" title="Validation holdout (recommend using the same splitting method as for test holdout)" expanded="false">
                    <expand macro="train_test_split_params" />
                </section>
                <section name="metrics" title="Metrics for evaluation" expanded="false">
                    <expand macro="scoring_selection" />
                </section>
            </when>
        </conditional>
        <expand macro="sl_mixed_input_plus_sequence" />
        <param name="save" type="select" multiple='true' display="checkboxes" label="Save the fitted model" optional="true" help="Evaluation scores will be output by default.">
            <option value="save_estimator" selected="true">Fitted estimator in skeleton and weights, separately</option>
            <option value="save_prediction">True labels and prediction results from evaluation for downstream analysis</option>
        </param>
    </inputs>
    <outputs>
        <data format="tabular" name="outfile_result" />
        <data format="zip" name="outfile_object" label="Fitted estimator or estimator skeleton on ${on_string}">
            <filter>str(save) and 'save_estimator' in str(save)</filter>
        </data>
        <data format="h5" name="outfile_weights" label="Weights trained on ${on_string}">
            <filter>str(save) and 'save_estimator' in str(save)</filter>

        </data>
    </outputs>
    <tests>
        <test>
            <conditional name="experiment_schemes">
                <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" />
                    <repeat name="param_set">
                        <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" />
                    </repeat>
                    <repeat name="param_set">
                        <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" />
                    </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" />
                    </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" />
                    </conditional>
                </section>
                <section name="metrics">
                    <conditional name="scoring">
                        <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="header1" value="true" />
            <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_estimator" />
            <output name="outfile_result">
                <assert_contents>
                    <has_n_columns n="2" />
                    <has_text text="0.638" />
                    <has_text text="-6.072" />
                </assert_contents>
            </output>
            <output name="outfile_object" file="train_test_eval_model01" compare="sim_size" delta="50" />
            <output name="outfile_weights" file="train_test_eval_weights01.h5" compare="sim_size" delta="50" />
        </test>
        <test>
            <conditional name="experiment_schemes">
                <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" />
                    <repeat name="param_set">
                        <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" />
                    </repeat>
                    <repeat name="param_set">
                        <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" />
                    </repeat>
                </section>
                <section name="test_split">
                    <conditional name="split_algos">
                        <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" />
                            <conditional name="column_selector_options_g">
                                <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" />
                    </conditional>
                </section>
                <section name="metrics">
                    <conditional name="scoring">
                        <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="header1" value="true" />
            <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_estimator,save_prediction" />
            <output name="outfile_result">
                <assert_contents>
                    <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="50" />
            <output name="outfile_y_true" file="keras_train_eval_y_true02.tabular" ftype="tabular" />
        </test>
        <test>
            <conditional name="experiment_schemes">
                <param name="selected_exp_scheme" value="train_val" />
                <param name="infile_estimator" value="pipeline10" ftype="zip" />
                <section name="hyperparams_swapping">
                    <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" />
                    </repeat>
                    <repeat name="param_set">
                        <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" />
                    </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" />
                    </conditional>
                </section>
                <section name="metrics">
                    <conditional name="scoring">
                        <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="header1" value="true" />
            <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="" />
            <output name="outfile_result" file="train_test_eval03.tabular" />
        </test>
    </tests>
    <help>
        <![CDATA[
**What it does**

- true labels or values and predicted values from the evaluation

        ]]>
    </help>
    <expand macro="sklearn_citation">
        <expand macro="keras_citation" />
    </expand>
</tool>