comparison feature_selection.xml @ 29:93f3b307485f draft

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

28:6d21b03e00a1

<tool id="sklearn_feature_selection" name="Feature Selection" version="@VERSION@">
    <description>module, including univariate filter selection methods and recursive feature elimination algorithm</description>
    <macros>
        <import>main_macros.xml</import>
    </macros>
    <expand macro="python_requirements"/>
    <!--TODO: Add imblearn package support-->
    <expand macro="macro_stdio"/>
    <version_command>echo "@VERSION@"</version_command>
    <command>
        <![CDATA[
        python "$feature_selection_script" '$inputs'
        ]]>

            ]]>
        </configfile>
    </configfiles>
    <inputs>
        <expand macro="feature_selection_fs"/>
        <param name="save" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Save the fitted selector?"/>
        <expand macro="sl_mixed_input_plus_sequence"/>
    </inputs>
    <outputs>
        <data format="tabular" name="outfile" />
        <data format="zip" name="outfile_selector" label="${fs_algorithm_selector.selected_algorithm}">
            <filter>save</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="selected_algorithm" value="SelectFromModel"/>
            <param name="input_mode" value="new"/>
            <param name="selected_module" value="ensemble"/>
            <param name="selected_estimator" value="RandomForestRegressor"/>
            <param name="text_params" value="n_estimators=10, random_state=10"/>
            <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
            <param name="header1" value="false"/>
            <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="header2" value="false"/>
            <output name="outfile" file="feature_selection_result01"/>
        </test>
        <test>
            <param name="selected_algorithm" value="GenericUnivariateSelect"/>
            <param name="param" value="20"/>
            <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="col2" value="1"/>
            <param name="header2" value="True"/>
            <output name="outfile" file="feature_selection_result02"/>
        </test>
        <test>
            <param name="selected_algorithm" value="SelectPercentile"/>
            <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="col2" value="1"/>
            <param name="header2" value="True"/>
            <output name="outfile" file="feature_selection_result03"/>
        </test>
        <test>
            <param name="selected_algorithm" value="SelectKBest"/>
            <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="col2" value="1"/>
            <param name="header2" value="True"/>
            <output name="outfile" file="feature_selection_result04"/>
        </test>
        <test>
            <param name="selected_algorithm" value="SelectFpr"/>
            <param name="alpha" value="0.05"/>
            <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="col2" value="1"/>
            <param name="header2" value="True"/>
            <output name="outfile" file="feature_selection_result05"/>
        </test>
        <test>
            <param name="selected_algorithm" value="SelectFdr"/>
            <param name="alpha" value="0.05"/>
            <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="col2" value="1"/>
            <param name="header2" value="True"/>
            <output name="outfile" file="feature_selection_result06"/>
        </test>
        <test>
            <param name="selected_algorithm" value="SelectFwe"/>
            <param name="alpha" value="0.05"/>
            <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="col2" value="1"/>
            <param name="header2" value="True"/>
            <output name="outfile" file="feature_selection_result07"/>
        </test>
        <test>
            <param name="selected_algorithm" value="RFE"/>
            <param name="input_mode" value="new"/>
            <param name="selected_module" value="ensemble"/>
            <param name="selected_estimator" value="RandomForestRegressor"/>
            <param name="text_params" value="n_estimators=10, random_state=10"/>
            <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
            <param name="header1" value="false"/>
            <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="header2" value="false"/>
            <output name="outfile" file="feature_selection_result08"/>
        </test>
        <test>
            <param name="selected_algorithm" value="RFECV"/>
            <param name="input_mode" value="new"/>
            <param name="selected_module" value="ensemble"/>
            <param name="selected_estimator" value="RandomForestRegressor"/>
            <param name="text_params" value="n_estimators=10, random_state=10"/>
            <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
            <param name="header1" value="false"/>
            <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="header2" value="false"/>
            <output name="outfile" file="feature_selection_result09"/>
        </test>
        <test>
            <param name="selected_algorithm" value="VarianceThreshold"/>
            <param name="threshold" value="0.1"/>
            <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="col2" value="1"/>
            <param name="header2" value="True"/>
            <output name="outfile" file="feature_selection_result10"/>
        </test>
        <test>
            <param name="selected_algorithm" value="SelectKBest"/>
            <param name="k" value="3"/>
            <param name="infile1" value="test3.tabular" ftype="tabular"/>
            <param name="header1" value="True"/>
            <param name="selected_column_selector_option" value="all_but_by_header_name"/>
            <param name="col1" value="target"/>
            <param name="infile2" value="test3.tabular" ftype="tabular"/>
            <param name="header2" value="True"/>
            <param name="selected_column_selector_option2" value="by_header_name"/>
            <param name="col2" value="target"/>
            <output name="outfile" file="feature_selection_result11"/>
        </test>
        <test>
            <param name="selected_algorithm" value="SelectFromModel"/>
            <param name="input_mode" value="prefitted"/>
            <param name="fitted_estimator" value="rfr_model01" ftype="zip"/>
            <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
            <param name="header1" value="false"/>
            <param name="col1" value="1,2,3,4,5"/>
            <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
            <param name="col2" value="1"/>
            <param name="header2" value="false"/>
            <output name="outfile" file="feature_selection_result12"/>
        </test>
        <test>
            <param name="selected_algorithm" value="RFECV"/>
            <param name="input_mode" value="new"/>
            <param name="selected_module" value="ensemble"/>
            <param name="selected_estimator" value="RandomForestRegressor"/>
            <param name="text_params" value="n_estimators=10, random_state=10"/>
            <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"/>
            </section>
            <param name="selected_cv" value="GroupShuffleSplit"/>
            <param name="random_state" value="0"/>
            <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="col2" value="1"/>
            <param name="header2" value="true"/>
            <output name="outfile" file="feature_selection_result13"/>
        </test>
    </tests>
    <help>
        <![CDATA[
**What it does**

.. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
        ]]>
    </help>
    <expand macro="sklearn_citation">
        <expand macro="skrebate_citation"/>
        <expand macro="xgboost_citation"/>
    </expand>
</tool>

29:93f3b307485f

<tool id="sklearn_feature_selection" name="Feature Selection" version="@VERSION@" profile="20.05">
    <description>module, including univariate filter selection methods and recursive feature elimination algorithm</description>
    <macros>
        <import>main_macros.xml</import>
    </macros>
    <expand macro="python_requirements" />
    <!--TODO: Add imblearn package support-->
    <expand macro="macro_stdio" />
    <version_command>echo "@VERSION@"</version_command>
    <command>
        <![CDATA[
        python "$feature_selection_script" '$inputs'
        ]]>

            ]]>
        </configfile>
    </configfiles>
    <inputs>
        <expand macro="feature_selection_fs" />
        <param name="save" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Save the fitted selector?" />
        <expand macro="sl_mixed_input_plus_sequence" />
    </inputs>
    <outputs>
        <data format="tabular" name="outfile" />
        <data format="zip" name="outfile_selector" label="${fs_algorithm_selector.selected_algorithm}">
            <filter>save</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="selected_algorithm" value="SelectFromModel" />
            <param name="input_mode" value="new" />
            <param name="selected_module" value="ensemble" />
            <param name="selected_estimator" value="RandomForestRegressor" />
            <param name="text_params" value="n_estimators=10, random_state=10" />
            <param name="infile1" value="regression_train.tabular" ftype="tabular" />
            <param name="header1" value="false" />
            <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="header2" value="false" />
            <output name="outfile" file="feature_selection_result01" />
        </test>
        <test>
            <param name="selected_algorithm" value="GenericUnivariateSelect" />
            <param name="param" value="20" />
            <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="col2" value="1" />
            <param name="header2" value="True" />
            <output name="outfile" file="feature_selection_result02" />
        </test>
        <test>
            <param name="selected_algorithm" value="SelectPercentile" />
            <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="col2" value="1" />
            <param name="header2" value="True" />
            <output name="outfile" file="feature_selection_result03" />
        </test>
        <test>
            <param name="selected_algorithm" value="SelectKBest" />
            <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="col2" value="1" />
            <param name="header2" value="True" />
            <output name="outfile" file="feature_selection_result04" />
        </test>
        <test>
            <param name="selected_algorithm" value="SelectFpr" />
            <param name="alpha" value="0.05" />
            <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="col2" value="1" />
            <param name="header2" value="True" />
            <output name="outfile" file="feature_selection_result05" />
        </test>
        <test>
            <param name="selected_algorithm" value="SelectFdr" />
            <param name="alpha" value="0.05" />
            <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="col2" value="1" />
            <param name="header2" value="True" />
            <output name="outfile" file="feature_selection_result06" />
        </test>
        <test>
            <param name="selected_algorithm" value="SelectFwe" />
            <param name="alpha" value="0.05" />
            <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="col2" value="1" />
            <param name="header2" value="True" />
            <output name="outfile" file="feature_selection_result07" />
        </test>
        <test>
            <param name="selected_algorithm" value="RFE" />
            <param name="input_mode" value="new" />
            <param name="selected_module" value="ensemble" />
            <param name="selected_estimator" value="RandomForestRegressor" />
            <param name="text_params" value="n_estimators=10, random_state=10" />
            <param name="infile1" value="regression_train.tabular" ftype="tabular" />
            <param name="header1" value="false" />
            <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="header2" value="false" />
            <output name="outfile" file="feature_selection_result08" />
        </test>
        <test>
            <param name="selected_algorithm" value="RFECV" />
            <param name="input_mode" value="new" />
            <param name="selected_module" value="ensemble" />
            <param name="selected_estimator" value="RandomForestRegressor" />
            <param name="text_params" value="n_estimators=10, random_state=10" />
            <param name="infile1" value="regression_train.tabular" ftype="tabular" />
            <param name="header1" value="false" />
            <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="header2" value="false" />
            <output name="outfile" file="feature_selection_result09" />
        </test>
        <test>
            <param name="selected_algorithm" value="VarianceThreshold" />
            <param name="threshold" value="0.1" />
            <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="col2" value="1" />
            <param name="header2" value="True" />
            <output name="outfile" file="feature_selection_result10" />
        </test>
        <test>
            <param name="selected_algorithm" value="SelectKBest" />
            <param name="k" value="3" />
            <param name="infile1" value="test3.tabular" ftype="tabular" />
            <param name="header1" value="True" />
            <param name="selected_column_selector_option" value="all_but_by_header_name" />
            <param name="col1" value="target" />
            <param name="infile2" value="test3.tabular" ftype="tabular" />
            <param name="header2" value="True" />
            <param name="selected_column_selector_option2" value="by_header_name" />
            <param name="col2" value="target" />
            <output name="outfile" file="feature_selection_result11" />
        </test>
        <test>
            <param name="selected_algorithm" value="SelectFromModel" />
            <param name="input_mode" value="prefitted" />
            <param name="fitted_estimator" value="rfr_model01" ftype="zip" />
            <param name="infile1" value="regression_train.tabular" ftype="tabular" />
            <param name="header1" value="false" />
            <param name="col1" value="1,2,3,4,5" />
            <param name="infile2" value="regression_train.tabular" ftype="tabular" />
            <param name="col2" value="1" />
            <param name="header2" value="false" />
            <output name="outfile" file="feature_selection_result12" />
        </test>
        <test>
            <param name="selected_algorithm" value="RFECV" />
            <param name="input_mode" value="new" />
            <param name="selected_module" value="ensemble" />
            <param name="selected_estimator" value="RandomForestRegressor" />
            <param name="text_params" value="n_estimators=10, random_state=10" />
            <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" />
            </section>
            <param name="selected_cv" value="GroupShuffleSplit" />
            <param name="random_state" value="0" />
            <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="col2" value="1" />
            <param name="header2" value="true" />
            <output name="outfile" file="feature_selection_result13" />
        </test>
    </tests>
    <help>
        <![CDATA[
**What it does**

.. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
        ]]>
    </help>
    <expand macro="sklearn_citation">
        <expand macro="skrebate_citation" />
        <expand macro="xgboost_citation" />
    </expand>
</tool>