diff pipeline.xml @ 19:4de3d598c116 draft

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

--- a/pipeline.xml	Fri Oct 02 08:49:25 2020 +0000
+++ b/pipeline.xml	Tue Apr 13 18:57:31 2021 +0000
@@ -1,10 +1,10 @@
-<tool id="sklearn_build_pipeline" name="Pipeline Builder" version="@VERSION@">
+<tool id="sklearn_build_pipeline" name="Pipeline Builder" version="@VERSION@" profile="20.05">
     <description>an all-in-one platform to build pipeline, single estimator, preprocessor and custom wrappers</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[
@@ -228,7 +228,7 @@
                     <option value="IRAPS">IRAPS -- feature selector and classifier</option>
                     <option value="preprocessors">Bio-sequence Encoders</option>
                 </param>
-                <when value="None"/>
+                <when value="None" />
                 <when value="pre_processor">
                     <conditional name="pre_processors">
                         <expand macro="sparse_preprocessors_ext" />
@@ -236,40 +236,38 @@
                     </conditional>
                 </when>
                 <when value="feature_selection">
-                    <expand macro="feature_selection_pipeline"/>
+                    <expand macro="feature_selection_pipeline" />
                 </when>
                 <when value="decomposition">
-                    <expand macro="matrix_decomposition_all"/>
+                    <expand macro="matrix_decomposition_all" />
                 </when>
                 <when value="kernel_approximation">
-                    <expand macro="kernel_approximation_all"/>
+                    <expand macro="kernel_approximation_all" />
                 </when>
                 <when value="FeatureAgglomeration">
-                    <expand macro="FeatureAgglomeration"/>
+                    <expand macro="FeatureAgglomeration" />
                 </when>
                 <when value="skrebate">
-                    <expand macro="skrebate"/>
+                    <expand macro="skrebate" />
                 </when>
                 <when value="imblearn">
-                    <expand macro="imbalanced_learn_sampling"/>
+                    <expand macro="imbalanced_learn_sampling" />
                 </when>
                 <when value="IRAPS">
-                    <expand macro="estimator_params_text"
-                        label="Type in parameter settings for IRAPSCore if different from default:"
-                        help="Default(=blank): n_iter=1000, responsive_thres=-1, resistant_thres=0, random_state=None. No double quotes"/>
-                    <param argument="p_thres" type="float" value="0.001" label="P value threshold" help="Float. default=0.001"/>
-                    <param argument="fc_thres" type="float" value="0.1" label="fold change threshold" help="Float. default=0.1"/>
-                    <param argument="occurrence" type="float" value="0.7" label="reservation factor" help="Float. default=0.7"/>
-                    <param argument="discretize" type="float" value="-1" label="The z_score threshold to discretize target value" help="Float. default=-1"/>
+                    <expand macro="estimator_params_text" label="Type in parameter settings for IRAPSCore if different from default:" help="Default(=blank): n_iter=1000, responsive_thres=-1, resistant_thres=0, random_state=None. No double quotes" />
+                    <param argument="p_thres" type="float" value="0.001" label="P value threshold" help="Float. default=0.001" />
+                    <param argument="fc_thres" type="float" value="0.1" label="fold change threshold" help="Float. default=0.1" />
+                    <param argument="occurrence" type="float" value="0.7" label="reservation factor" help="Float. default=0.7" />
+                    <param argument="discretize" type="float" value="-1" label="The z_score threshold to discretize target value" help="Float. default=-1" />
                 </when>
                 <when value="preprocessors">
-                    <expand macro="preprocessors_sequence_encoders"/>
+                    <expand macro="preprocessors_sequence_encoders" />
                 </when>
             </conditional>
         </repeat>
         <section name="final_estimator" title="Final Estimator" expanded="true">
             <conditional name="estimator_selector">
-                <param name="selected_module" type="select" label="Choose the module that contains target estimator:" >
+                <param name="selected_module" type="select" label="Choose the module that contains target estimator:">
                     <expand macro="estimator_module_options">
                         <option value="sklearn.compose">sklearn.compose</option>
                         <option value="binarize_target">Binarize Target Classifier or Regressor</option>
@@ -282,23 +280,23 @@
                         <param name="selected_estimator" type="select" label="Choose estimator class:">
                             <option value="TransformedTargetRegressor" selected="true">TransformedTargetRegressor</option>
                         </param>
-                        <param name="regressor" type="data" format="zip" label="Choose the dataset containing the wrapped regressor"/>
-                        <param name="transformer" type="data" format="zip" label="Choose the dataset containing transformer"/>
+                        <param name="regressor" type="data" format="zip" label="Choose the dataset containing the wrapped regressor" />
+                        <param name="transformer" type="data" format="zip" label="Choose the dataset containing transformer" />
                     </when>
                     <when value="binarize_target">
                         <param name="clf_or_regr" type="select" label="Classifier or Regressor:">
                             <option value="BinarizeTargetClassifier">BinarizeTargetClassifier</option>
                             <option value="BinarizeTargetRegressor">BinarizeTargetRegressor</option>
                         </param>
-                        <param name="wrapped_estimator" type="data" format="zip" label="Choose the dataset containing the wrapped estimator or pipeline"/>
-                        <param name='z_score' type="float" value="-1" optional="false" label="Discrize target values using z_score"/>
-                        <param name='value' type="float" value="" optional="true" label="Discretize target values using a fixed value instead" help="Optional. default: None."/>
-                        <param name="less_is_positive" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Are the detecting values smaller than others?"/>
+                        <param name="wrapped_estimator" type="data" format="zip" label="Choose the dataset containing the wrapped estimator or pipeline" />
+                        <param name='z_score' type="float" value="-1" optional="false" label="Discrize target values using z_score" />
+                        <param name='value' type="float" value="" optional="true" label="Discretize target values using a fixed value instead" help="Optional. default: None." />
+                        <param name="less_is_positive" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Are the detecting values smaller than others?" />
                     </when>
                     <when value="custom_estimator">
-                        <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline"/>
+                        <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline" />
                     </when>
-                    <when value="none"/>
+                    <when value="none" />
                 </expand>
             </conditional>
         </section>
@@ -306,11 +304,10 @@
             <option value="Pipeline_Builder" selected="true">Pipeline</option>
             <option value="Final_Estimator_Builder">Final Estimator</option>
         </param>-->
-        <param name="get_params" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Output parameters for searchCV?"
-                help="Optional. Tunable parameters could be obtained through `estimator_attributes` tool."/>
+        <param name="get_params" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Output parameters for searchCV?" help="Optional. Tunable parameters could be obtained through `estimator_attributes` tool." />
     </inputs>
     <outputs>
-        <data format="zip" name="outfile" label="New Pipleline/Estimator"/>
+        <data format="zip" name="outfile" label="New Pipleline/Estimator" />
         <data format="tabular" name="outfile_params" label="get_params for Pipleline/Estimator">
             <filter>get_params</filter>
         </data>
@@ -318,246 +315,246 @@
     <tests>
         <test>
             <conditional name="component_selector">
-                <param name="component_type" value="pre_processor"/>
+                <param name="component_type" value="pre_processor" />
                 <conditional name="pre_processors">
-                    <param name="selected_pre_processor" value="QuantileTransformer"/>
+                    <param name="selected_pre_processor" value="QuantileTransformer" />
                     <section name="options">
-                        <param name="random_state" value="10"/>
+                        <param name="random_state" value="10" />
                     </section>
                 </conditional>
             </conditional>
             <section name="final_estimator">
                 <conditional name="estimator_selector">
-                    <param name="selected_module" value="none"/>
+                    <param name="selected_module" value="none" />
                 </conditional>
             </section>
-            <output name="outfile" file="pipeline17" compare="sim_size" delta="5"/>
+            <output name="outfile" file="pipeline17" compare="sim_size" delta="30" />
         </test>
         <test>
             <conditional name="component_selector">
-                <param name="component_type" value="pre_processor"/>
+                <param name="component_type" value="pre_processor" />
                 <conditional name="pre_processors">
-                    <param name="selected_pre_processor" value="PowerTransformer"/>
+                    <param name="selected_pre_processor" value="PowerTransformer" />
                 </conditional>
             </conditional>
             <section name="final_estimator">
                 <conditional name="estimator_selector">
-                    <param name="selected_module" value="sklearn.compose"/>
-                    <param name="regressor" value="RandomForestRegressor01.zip" ftype="zip"/>
-                    <param name="transformer" value="pipeline17" ftype="zip"/>
+                    <param name="selected_module" value="sklearn.compose" />
+                    <param name="regressor" value="RandomForestRegressor01.zip" ftype="zip" />
+                    <param name="transformer" value="pipeline17" ftype="zip" />
                 </conditional>
             </section>
-            <param name="get_params" value="true"/>
-            <output name="outfile_params" file="pipeline_params18" ftype="tabular"/>
+            <param name="get_params" value="true" />
+            <output name="outfile_params" file="pipeline_params18" ftype="tabular" />
         </test>
         <test>
             <repeat name="pipeline_component">
                 <conditional name="component_selector">
-                    <param name="component_type" value="pre_processor"/>
+                    <param name="component_type" value="pre_processor" />
                     <conditional name="pre_processors">
-                        <param name="selected_pre_processor" value="RobustScaler"/>
+                        <param name="selected_pre_processor" value="RobustScaler" />
                     </conditional>
                 </conditional>
             </repeat>
             <repeat name="pipeline_component">
                 <conditional name="component_selector">
-                    <param name="component_type" value="feature_selection"/>
+                    <param name="component_type" value="feature_selection" />
                     <conditional name="fs_algorithm_selector">
-                        <param name="selected_algorithm" value="SelectKBest"/>
-                        <param name="score_func" value="f_classif"/>
+                        <param name="selected_algorithm" value="SelectKBest" />
+                        <param name="score_func" value="f_classif" />
                     </conditional>
                 </conditional>
             </repeat>
-            <param name="selected_module" value="svm"/>
-            <param name="selected_estimator" value="SVR"/>
-            <param name="text_params" value="kernel='linear'"/>
-            <output name="outfile" file="pipeline01" compare="sim_size" delta="5"/>
+            <param name="selected_module" value="svm" />
+            <param name="selected_estimator" value="SVR" />
+            <param name="text_params" value="kernel='linear'" />
+            <output name="outfile" file="pipeline01" compare="sim_size" delta="30" />
         </test>
         <test>
             <conditional name="component_selector">
-                <param name="component_type" value="pre_processor"/>
+                <param name="component_type" value="pre_processor" />
                 <conditional name="pre_processors">
-                    <param name="selected_pre_processor" value="RobustScaler"/>
+                    <param name="selected_pre_processor" value="RobustScaler" />
                 </conditional>
             </conditional>
-            <param name="selected_module" value="linear_model"/>
-            <param name="selected_estimator" value="LassoCV"/>
-            <output name="outfile" file="pipeline02" compare="sim_size" delta="5"/>
+            <param name="selected_module" value="linear_model" />
+            <param name="selected_estimator" value="LassoCV" />
+            <output name="outfile" file="pipeline02" compare="sim_size" delta="30" />
         </test>
         <test>
             <conditional name="component_selector">
-                <param name="component_type" value="pre_processor"/>
+                <param name="component_type" value="pre_processor" />
                 <conditional name="pre_processors">
-                    <param name="selected_pre_processor" value="RobustScaler"/>
+                    <param name="selected_pre_processor" value="RobustScaler" />
                 </conditional>
             </conditional>
-            <param name="selected_module" value="xgboost"/>
-            <param name="selected_estimator" value="XGBClassifier"/>
-            <output name="outfile" file="pipeline03" compare="sim_size" delta="5"/>
+            <param name="selected_module" value="xgboost" />
+            <param name="selected_estimator" value="XGBClassifier" />
+            <output name="outfile" file="pipeline03" compare="sim_size" delta="30" />
         </test>
         <test>
             <conditional name="component_selector">
-                <param name="component_type" value="feature_selection"/>
+                <param name="component_type" value="feature_selection" />
                 <conditional name="fs_algorithm_selector">
-                    <param name="selected_algorithm" value="SelectFromModel"/>
+                    <param name="selected_algorithm" value="SelectFromModel" />
                     <conditional name="model_inputter">
                         <conditional name="estimator_selector">
-                            <param name="selected_module" value="ensemble"/>
-                            <param name="selected_estimator" value="AdaBoostClassifier"/>
+                            <param name="selected_module" value="ensemble" />
+                            <param name="selected_estimator" value="AdaBoostClassifier" />
                         </conditional>
                     </conditional>
                 </conditional>
             </conditional>
             <section name="final_estimator">
-                <param name="selected_module" value="svm"/>
-                <param name="selected_estimator" value="LinearSVC"/>
+                <param name="selected_module" value="svm" />
+                <param name="selected_estimator" value="LinearSVC" />
             </section>
-            <output name="outfile" file="pipeline04" compare="sim_size" delta="5"/>
+            <output name="outfile" file="pipeline04" compare="sim_size" delta="30" />
         </test>
         <test>
             <conditional name="component_selector">
-                <param name="component_type" value="None"/>
+                <param name="component_type" value="None" />
             </conditional>
-            <param name="selected_module" value="ensemble"/>
-            <param name="selected_estimator" value="RandomForestRegressor"/>
-            <param name="text_params" value="n_estimators=100, random_state=42"/>
-            <param name="get_params" value="true"/>
-            <output name="outfile" file="pipeline05" compare="sim_size" delta="5"/>
-            <output name="outfile_params" file="pipeline_params05.tabular" ftype="tabular"/>
+            <param name="selected_module" value="ensemble" />
+            <param name="selected_estimator" value="RandomForestRegressor" />
+            <param name="text_params" value="n_estimators=100, random_state=42" />
+            <param name="get_params" value="true" />
+            <output name="outfile" file="pipeline05" compare="sim_size" delta="30" />
+            <output name="outfile_params" file="pipeline_params05.tabular" ftype="tabular" />
         </test>
         <test>
             <conditional name="component_selector">
-                <param name="component_type" value="decomposition"/>
-                    <conditional name="matrix_decomposition_selector">
-                        <param name="select_algorithm" value="PCA"/>
-                    </conditional>
+                <param name="component_type" value="decomposition" />
+                <conditional name="matrix_decomposition_selector">
+                    <param name="select_algorithm" value="PCA" />
+                </conditional>
             </conditional>
-            <param name="selected_module" value="ensemble"/>
-            <param name="selected_estimator" value="AdaBoostRegressor"/>
-            <output name="outfile" file="pipeline06" compare="sim_size" delta="5"/>
+            <param name="selected_module" value="ensemble" />
+            <param name="selected_estimator" value="AdaBoostRegressor" />
+            <output name="outfile" file="pipeline06" compare="sim_size" delta="30" />
         </test>
         <test>
             <conditional name="component_selector">
-                <param name="component_type" value="kernel_approximation"/>
-                    <conditional name="kernel_approximation_selector">
-                        <param name="select_algorithm" value="RBFSampler"/>
-                        <param name="text_params" value="n_components=10, gamma=2.0"/>
-                    </conditional>
+                <param name="component_type" value="kernel_approximation" />
+                <conditional name="kernel_approximation_selector">
+                    <param name="select_algorithm" value="RBFSampler" />
+                    <param name="text_params" value="n_components=10, gamma=2.0" />
+                </conditional>
             </conditional>
-            <param name="selected_module" value="ensemble"/>
-            <param name="selected_estimator" value="AdaBoostClassifier"/>
-            <output name="outfile" file="pipeline07" compare="sim_size" delta="5"/>
+            <param name="selected_module" value="ensemble" />
+            <param name="selected_estimator" value="AdaBoostClassifier" />
+            <output name="outfile" file="pipeline07" compare="sim_size" delta="30" />
         </test>
         <test>
             <conditional name="component_selector">
-                <param name="component_type" value="FeatureAgglomeration"/>
-                    <conditional name="FeatureAgglomeration_selector">
-                        <param name="select_algorithm" value="FeatureAgglomeration"/>
-                        <param name="text_params" value="n_clusters=3, affinity='euclidean'"/>
-                    </conditional>
+                <param name="component_type" value="FeatureAgglomeration" />
+                <conditional name="FeatureAgglomeration_selector">
+                    <param name="select_algorithm" value="FeatureAgglomeration" />
+                    <param name="text_params" value="n_clusters=3, affinity='euclidean'" />
+                </conditional>
             </conditional>
-            <param name="selected_module" value="ensemble"/>
-            <param name="selected_estimator" value="AdaBoostClassifier"/>
-            <output name="outfile" file="pipeline08" compare="sim_size" delta="20"/>
+            <param name="selected_module" value="ensemble" />
+            <param name="selected_estimator" value="AdaBoostClassifier" />
+            <output name="outfile" file="pipeline08" compare="sim_size" delta="30" />
         </test>
         <test>
             <conditional name="component_selector">
-                <param name="component_type" value="skrebate"/>
-                    <conditional name="skrebate_selector">
-                        <param name="select_algorithm" value="ReliefF"/>
-                        <param name="text_params" value="n_features_to_select=3, n_neighbors=100"/>
-                    </conditional>
+                <param name="component_type" value="skrebate" />
+                <conditional name="skrebate_selector">
+                    <param name="select_algorithm" value="ReliefF" />
+                    <param name="text_params" value="n_features_to_select=3, n_neighbors=100" />
+                </conditional>
             </conditional>
-            <param name="selected_module" value="ensemble"/>
-            <param name="selected_estimator" value="RandomForestRegressor"/>
-            <output name="outfile" file="pipeline09" compare="sim_size" delta="5"/>
+            <param name="selected_module" value="ensemble" />
+            <param name="selected_estimator" value="RandomForestRegressor" />
+            <output name="outfile" file="pipeline09" compare="sim_size" delta="30" />
         </test>
         <test>
             <conditional name="component_selector">
-                <param name="component_type" value="imblearn"/>
+                <param name="component_type" value="imblearn" />
                 <conditional name="imblearn_selector">
-                    <param name="select_algorithm" value="under_sampling.EditedNearestNeighbours"/>
+                    <param name="select_algorithm" value="under_sampling.EditedNearestNeighbours" />
                 </conditional>
             </conditional>
-            <param name="selected_module" value="ensemble"/>
-            <param name="selected_estimator" value="RandomForestClassifier"/>
-            <output name="outfile" file="pipeline11" compare="sim_size" delta="5"/>
+            <param name="selected_module" value="ensemble" />
+            <param name="selected_estimator" value="RandomForestClassifier" />
+            <output name="outfile" file="pipeline11" compare="sim_size" delta="30" />
         </test>
         <test expect_failure="true">
             <conditional name="component_selector">
-                <param name="component_type" value="None"/>
+                <param name="component_type" value="None" />
             </conditional>
-            <param name="selected_module" value="ensemble"/>
-            <param name="selected_estimator" value="RandomForestRegressor"/>
-            <param name="text_params" value="n_estimators=__import__('os').system('ls ~')"/>
+            <param name="selected_module" value="ensemble" />
+            <param name="selected_estimator" value="RandomForestRegressor" />
+            <param name="text_params" value="n_estimators=__import__('os').system('ls ~')" />
         </test>
         <test>
             <conditional name="component_selector">
-                <param name="component_type" value="feature_selection"/>
+                <param name="component_type" value="feature_selection" />
                 <conditional name="fs_algorithm_selector">
-                    <param name="selected_algorithm" value="RFE"/>
+                    <param name="selected_algorithm" value="RFE" />
                     <conditional name="estimator_selector">
-                        <param name="selected_module" value="xgboost"/>
-                        <param name="selected_estimator" value="XGBRegressor"/>
-                        <param name="text_params" value="random_state=0"/>
+                        <param name="selected_module" value="xgboost" />
+                        <param name="selected_estimator" value="XGBRegressor" />
+                        <param name="text_params" value="random_state=0" />
                     </conditional>
                 </conditional>
             </conditional>
             <section name="final_estimator">
                 <conditional name="estimator_selector">
-                    <param name="selected_module" value="none"/>
+                    <param name="selected_module" value="none" />
                 </conditional>
             </section>
-            <output name="outfile" file="pipeline12" compare="sim_size" delta="5"/>
+            <output name="outfile" file="pipeline12" compare="sim_size" delta="30" />
         </test>
         <test>
             <conditional name="component_selector">
-                <param name="component_type" value="None"/>
+                <param name="component_type" value="None" />
             </conditional>
-            <param name="selected_module" value="ensemble"/>
-            <param name="selected_estimator" value="RandomForestClassifier"/>
-            <output name="outfile" file="RandomForestClassifier.zip" compare="sim_size" delta="5"/>
+            <param name="selected_module" value="ensemble" />
+            <param name="selected_estimator" value="RandomForestClassifier" />
+            <output name="outfile" file="RandomForestClassifier.zip" compare="sim_size" delta="30" />
         </test>
         <test>
             <conditional name="component_selector">
-                <param name="component_type" value="IRAPS"/>
+                <param name="component_type" value="IRAPS" />
             </conditional>
             <section name="final_estimator">
                 <conditional name="estimator_selector">
-                    <param name="selected_module" value="none"/>
+                    <param name="selected_module" value="none" />
                 </conditional>
             </section>
-            <output name="outfile" file="pipeline14" compare="sim_size" delta="5"/>
+            <output name="outfile" file="pipeline14" compare="sim_size" delta="30" />
         </test>
         <test>
             <conditional name="component_selector">
-                <param name="component_type" value="None"/>
+                <param name="component_type" value="None" />
             </conditional>
             <section name="final_estimator">
                 <conditional name="estimator_selector">
-                    <param name="selected_module" value="binarize_target"/>
-                    <param name="clf_or_regr" value="BinarizeTargetClassifier"/>
-                    <param name="wrapped_estimator" value="RandomForestClassifier.zip" ftype="zip"/>
+                    <param name="selected_module" value="binarize_target" />
+                    <param name="clf_or_regr" value="BinarizeTargetClassifier" />
+                    <param name="wrapped_estimator" value="RandomForestClassifier.zip" ftype="zip" />
                 </conditional>
             </section>
-            <output name="outfile" file="pipeline15" compare="sim_size" delta="5"/>
+            <output name="outfile" file="pipeline15" compare="sim_size" delta="30" />
         </test>
         <test>
             <conditional name="component_selector">
-                <param name="component_type" value="preprocessors"/>
+                <param name="component_type" value="preprocessors" />
                 <conditional name="encoder_selection">
-                    <param name="encoder_type" value="GenomeOneHotEncoder"/>
-                    <param name="seq_length" value="1000"/>
-                    <param name="padding" value="True"/>
+                    <param name="encoder_type" value="GenomeOneHotEncoder" />
+                    <param name="seq_length" value="1000" />
+                    <param name="padding" value="True" />
                 </conditional>
             </conditional>
             <section name="final_estimator">
                 <conditional name="estimator_selector">
-                    <param name="selected_module" value="custom_estimator"/>
-                    <param name="c_estimator" value="keras_model02" ftype="zip"/>
+                    <param name="selected_module" value="custom_estimator" />
+                    <param name="c_estimator" value="keras_model02" ftype="zip" />
                 </conditional>
             </section>
-            <output name="outfile" file="pipeline16" compare="sim_size" delta="5"/>
+            <output name="outfile" file="pipeline16" compare="sim_size" delta="30" />
         </test>
     </tests>
     <help>
@@ -616,8 +613,8 @@
         ]]>
     </help>
     <expand macro="sklearn_citation">
-        <expand macro="skrebate_citation"/>
-        <expand macro="xgboost_citation"/>
-        <expand macro="imblearn_citation"/>
+        <expand macro="skrebate_citation" />
+        <expand macro="xgboost_citation" />
+        <expand macro="imblearn_citation" />
     </expand>
 </tool>