Repository 'sklearn_searchcv'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv

Changeset 6:7509d7059040 (2018-10-11)
Previous changeset 5:0987bc3904a0 (2018-09-29) Next changeset 7:4368259ff821 (2018-12-30)
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
modified:
search_model_validation.xml
test-data/glm_model08
test-data/glm_result08
added:
test-data/abc_model01
test-data/abc_result01
test-data/abr_model01
test-data/abr_result01
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diff -r 0987bc3904a0 -r 7509d7059040 search_model_validation.xml
--- a/search_model_validation.xml Sat Sep 29 07:26:39 2018 -0400
+++ b/search_model_validation.xml Thu Oct 11 03:30:01 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>
         <![CDATA[
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diff -r 0987bc3904a0 -r 7509d7059040 test-data/abc_model01
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Binary file test-data/abc_model01 has changed
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diff -r 0987bc3904a0 -r 7509d7059040 test-data/abc_result01
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abc_result01 Thu Oct 11 03:30:01 2018 -0400
b
@@ -0,0 +1,6 @@
+0 1 2 3 predicted
+3.68258022948 2.82110345641 -3.9901407239999998 -1.9523364774 1
+0.015942057224 -0.7119585943469999 0.125502976978 -0.972218263337 0
+2.0869076882499997 0.929399321468 -2.1292408448400004 -1.9971402218799998 1
+1.4132105208399999 0.523750660422 -1.4210539291 -1.49298569451 1
+0.7683140439399999 1.38267855169 -0.989045048734 0.649504257894 1
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diff -r 0987bc3904a0 -r 7509d7059040 test-data/abr_model01
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Binary file test-data/abr_model01 has changed
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diff -r 0987bc3904a0 -r 7509d7059040 test-data/abr_result01
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abr_result01 Thu Oct 11 03:30:01 2018 -0400
b
@@ -0,0 +1,6 @@
+0 1 2 3 4 predicted
+86.97021227350001 1.00532111569 -1.01739601979 -0.613139481654 0.641846874331 0.323842059244
+91.2021798817 -0.6215229712070001 1.11914889596 0.390012184498 1.28956938152 1.1503117056799999
+-47.4101632272 -0.638416457964 -0.7327774684530001 -0.8640261049779999 -1.06109770116 -0.7191695359690001
+61.712804630200004 -1.0999480057700002 -0.739679672932 0.585657963012 1.4890682753600002 1.1503117056799999
+-206.998295124 0.130238853011 0.70574123041 1.3320656526399999 -1.3322092373799999 -0.7191695359690001
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diff -r 0987bc3904a0 -r 7509d7059040 test-data/glm_model08
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Binary file test-data/glm_model08 has changed
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diff -r 0987bc3904a0 -r 7509d7059040 test-data/glm_result08
--- a/test-data/glm_result08 Sat Sep 29 07:26:39 2018 -0400
+++ b/test-data/glm_result08 Thu Oct 11 03:30:01 2018 -0400
b
@@ -1,5 +1,5 @@
-3.68258022948 2.82110345641 -3.9901407239999998 -1.9523364774 1
+3.68258022948 2.82110345641 -3.9901407239999998 -1.9523364774 0
 0.015942057224 -0.7119585943469999 0.125502976978 -0.972218263337 0
-2.0869076882499997 0.929399321468 -2.1292408448400004 -1.9971402218799998 1
-1.4132105208399999 0.523750660422 -1.4210539291 -1.49298569451 1
+2.0869076882499997 0.929399321468 -2.1292408448400004 -1.9971402218799998 0
+1.4132105208399999 0.523750660422 -1.4210539291 -1.49298569451 0
 0.7683140439399999 1.38267855169 -0.989045048734 0.649504257894 1