diff feature_selection.xml @ 29:93f3b307485f draft

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

--- a/feature_selection.xml	Thu Oct 01 20:56:31 2020 +0000
+++ b/feature_selection.xml	Tue Apr 13 18:21:34 2021 +0000
@@ -1,11 +1,11 @@
-<tool id="sklearn_feature_selection" name="Feature Selection" version="@VERSION@">
+<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"/>
+    <expand macro="python_requirements" />
     <!--TODO: Add imblearn package support-->
-    <expand macro="macro_stdio"/>
+    <expand macro="macro_stdio" />
     <version_command>echo "@VERSION@"</version_command>
     <command>
         <![CDATA[
@@ -150,9 +150,9 @@
         </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"/>
+        <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" />
@@ -162,168 +162,168 @@
     </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"/>
+            <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"/>
+            <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"/>
+            <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"/>
+            <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"/>
+            <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"/>
+            <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"/>
+            <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"/>
+            <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"/>
+            <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"/>
+            <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"/>
+            <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"/>
+            <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"/>
+            <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"/>
+                <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"/>
+            <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>
@@ -337,7 +337,7 @@
         ]]>
     </help>
     <expand macro="sklearn_citation">
-        <expand macro="skrebate_citation"/>
-        <expand macro="xgboost_citation"/>
+        <expand macro="skrebate_citation" />
+        <expand macro="xgboost_citation" />
     </expand>
 </tool>