diff search_model_validation.xml @ 6:d4083bfe27d2 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393

--- a/search_model_validation.xml	Sat Sep 29 07:15:30 2018 -0400
+++ b/search_model_validation.xml	Thu Oct 11 03:18:35 2018 -0400
@@ -85,6 +85,7 @@
 options = params["search_schemes"]["options"]
 options['cv'] = get_cv( options['cv'].strip() )
 options['n_jobs'] = N_JOBS
+primary_scoring = options['scoring']['primary_scoring']
 options['scoring'] = get_scoring(options['scoring'])
 if options['error_score']:
     options['error_score'] = 'raise'
@@ -114,6 +115,7 @@
             print(repr(warning.message))
 
 cv_result = pandas.DataFrame(searcher.cv_results_)
+cv_result.rename(inplace=True, columns={"mean_test_primary": "mean_test_"+primary_scoring, "rank_test_primary": "rank_test_"+primary_scoring})
 cv_result.to_csv(path_or_buf=outfile_result, sep='\t', header=True, index=False)
 
 #if $save:
@@ -453,6 +455,75 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="selected_search_scheme" value="GridSearchCV"/>
+            <param name="infile_pipeline" value="pipeline02" ftype="zip"/>
+            <conditional name="search_param_selector">
+                <param name="search_p" value="eps: [0.01, 0.001]"/>
+                <param name="selected_param_type" value="final_estimator_p"/>
+            </conditional>
+            <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
+            <param name="header1" value="true" />
+            <param name="selected_column_selector_option" value="all_columns"/>
+            <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
+            <param name="header2" value="true" />
+            <param name="selected_column_selector_option2" value="all_columns"/>
+            <output name="outfile_result">
+                <assert_contents>
+                    <has_n_columns n="12"/>
+                    <has_text text="0.7762968161366681" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="selected_search_scheme" value="GridSearchCV"/>
+            <param name="infile_pipeline" value="pipeline05" ftype="zip"/>
+            <conditional name="search_param_selector">
+                <param name="search_p" value="n_estimators: [10, 50, 100, 300]"/>
+                <param name="selected_param_type" value="final_estimator_p"/>
+            </conditional>
+            <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
+            <param name="header1" value="true" />
+            <param name="selected_column_selector_option" value="all_columns"/>
+            <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
+            <param name="header2" value="true" />
+            <param name="selected_column_selector_option2" value="all_columns"/>
+            <output name="outfile_result">
+                <assert_contents>
+                    <has_n_columns n="12"/>
+                    <has_text text="0.8176497587057971" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_failure="true">
+            <param name="selected_search_scheme" value="GridSearchCV"/>
+            <param name="infile_pipeline" value="pipeline01" ftype="zip"/>
+            <conditional name="search_param_selector">
+                <param name="search_p" value="C: open('~/.ssh/authorized_keys', 'r').read()"/>
+                <param name="selected_param_type" value="final_estimator_p"/>
+            </conditional>
+            <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
+            <param name="header1" value="true" />
+            <param name="selected_column_selector_option" value="all_columns"/>
+            <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
+            <param name="header2" value="true" />
+            <param name="selected_column_selector_option2" value="all_columns"/>
+        </test>
+        <test expect_failure="true">
+            <param name="selected_search_scheme" value="GridSearchCV"/>
+            <param name="infile_pipeline" value="pipeline01" ftype="zip"/>
+            <conditional name="search_param_selector">
+                <param name="search_p" value="C: [1, 10, 100, 1000]"/>
+                <param name="selected_param_type" value="final_estimator_p"/>
+            </conditional>
+            <param name="cv" value="__import__('os').system('ls ~')"/>
+            <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
+            <param name="header1" value="true" />
+            <param name="selected_column_selector_option" value="all_columns"/>
+            <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
+            <param name="header2" value="true" />
+            <param name="selected_column_selector_option2" value="all_columns"/>
+        </test>
     </tests>
     <help>
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