diff keras_train_and_eval.xml @ 4:3866911c93ae draft

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

--- a/keras_train_and_eval.xml	Thu Oct 01 21:12:39 2020 +0000
+++ b/keras_train_and_eval.xml	Tue Apr 13 18:37:35 2021 +0000
@@ -1,11 +1,11 @@
-<tool id="keras_train_and_eval" name="Deep learning training and evaluation" version="@VERSION@">
+<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"/>
+    <expand macro="python_requirements" />
+    <expand macro="macro_stdio" />
     <version_command>echo "@VERSION@"</version_command>
     <command>
         <![CDATA[
@@ -19,30 +19,27 @@
             --inputs '$inputs'
             --estimator '$experiment_schemes.infile_estimator'
             #if $input_options.selected_input == 'seq_fasta'
-            --fasta_path '$input_options.fasta_path'
+                --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"
+                --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'
+                --infile1 '$input_options.infile1'
             #end if
-            --infile2 '$input_options.infile2'
-            --outfile_result "`pwd`/tmp_outfile_result"
+                --infile2 '$input_options.infile2'
+                --outfile_result '$outfile_result'
             #if $save and 'save_estimator' in str($save)
-            --outfile_object '$outfile_object'
-            --outfile_weights '$outfile_weights'
+                --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'
+                --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'
+                --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>
@@ -55,39 +52,39 @@
                 <option value="train_val_test">Train, Validate and and Evaluate</option>
             </param>
             <when value="train_val">
-                <expand macro="estimator_and_hyperparameter"/>
+                <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 macro="cv_groups" />
                     </expand>
                 </section>
                 <section name="metrics" title="Metrics for evaluation" expanded="false">
-                    <expand macro="scoring_selection"/>
+                    <expand macro="scoring_selection" />
                 </section>
             </when>
             <when value="train_val_test">
-                <expand macro="estimator_and_hyperparameter"/>
+                <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 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"/>
+                    <expand macro="train_test_split_params" />
                 </section>
                 <section name="metrics" title="Metrics for evaluation" expanded="false">
-                    <expand macro="scoring_selection"/>
+                    <expand macro="scoring_selection" />
                 </section>
             </when>
         </conditional>
-        <expand macro="sl_mixed_input_plus_sequence"/>
+        <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="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>
@@ -104,176 +101,176 @@
     <tests>
         <test>
             <conditional name="experiment_schemes">
-                <param name="selected_exp_scheme" value="train_val_test"/>
-                <param name="infile_estimator" value="keras_model04" ftype="zip"/>
+                <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"/>
+                    <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"/>
+                        <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"/>
+                        <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"/>
+                        <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"/>
+                        <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"/>
+                        <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"/>
+                        <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"/>
+                        <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="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="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"/>
+            <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"/>
+                    <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="5"/>
-            <output name="outfile_weights" file="train_test_eval_weights01.h5" compare="sim_size" delta="5"/>
+            <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"/>
+                <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"/>
+                    <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"/>
+                        <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"/>
+                        <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"/>
+                        <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"/>
+                        <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"/>
+                        <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"/>
+                            <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"/>
+                                <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"/>
+                        <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"/>
+                        <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="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="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" >
+            <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"/>
+                    <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="5"/>
-            <output name="outfile_y_true" file="keras_train_eval_y_true02.tabular" ftype="tabular"/>
+            <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"/>
+                <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"/>
+                    <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"/>
+                        <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"/>
+                        <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"/>
+                        <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"/>
+                        <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"/>
+                        <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="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="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"/>
+            <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>
@@ -307,6 +304,6 @@
         ]]>
     </help>
     <expand macro="sklearn_citation">
-        <expand macro="keras_citation"/>
+        <expand macro="keras_citation" />
     </expand>
 </tool>