diff search_model_validation.xml @ 4:2e6540c11251 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1

--- a/search_model_validation.xml	Fri Aug 17 12:26:17 2018 -0400
+++ b/search_model_validation.xml	Thu Aug 23 16:14:26 2018 -0400
@@ -21,11 +21,12 @@
 import os
 import json
 import pandas
-import pickle
+import skrebate
 from sklearn import model_selection
 from sklearn.exceptions import FitFailedWarning
 
-execfile("$__tool_directory__/utils.py")
+execfile("$__tool_directory__/sk_whitelist.py")
+execfile("$__tool_directory__/utils.py", globals())
 
 warnings.simplefilter('ignore')
 
@@ -94,7 +95,8 @@
     options['pre_dispatch'] = None
 
 with open(infile_pipeline, 'rb') as pipeline_handler:
-    pipeline = pickle.load(pipeline_handler)
+    pipeline = SafePickler.load(pipeline_handler)
+
 search_params = get_search_params(params_builder)
 searcher = optimizers(pipeline, search_params, **options)
 
@@ -151,7 +153,7 @@
     <tests>
         <test>
             <param name="selected_search_scheme" value="GridSearchCV"/>
-            <param name="infile_pipeline" value="pipeline01"/>
+            <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"/>
@@ -176,7 +178,7 @@
         </test>
         <test>
             <param name="selected_search_scheme" value="RandomizedSearchCV"/>
-            <param name="infile_pipeline" value="pipeline01"/>
+            <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"/>
@@ -208,7 +210,7 @@
         </test>
         <test>
             <param name="selected_search_scheme" value="RandomizedSearchCV"/>
-            <param name="infile_pipeline" value="pipeline03"/>
+            <param name="infile_pipeline" value="pipeline03" ftype="zip"/>
             <conditional name="search_param_selector">
                 <param name="search_p" value="n_estimators: np_arange(50, 1001, 50)"/>
                 <param name="selected_param_type" value="final_estimator_p"/>
@@ -240,7 +242,7 @@
         </test>
         <test>
             <param name="selected_search_scheme" value="GridSearchCV"/>
-            <param name="infile_pipeline" value="pipeline04"/>
+            <param name="infile_pipeline" value="pipeline04" ftype="zip"/>
             <conditional name="search_param_selector">
                 <param name="search_p" value="random_state: list(range(100, 1001, 100))"/>
                 <param name="selected_param_type" value="final_estimator_p"/>
@@ -264,7 +266,7 @@
         </test>
         <test>
             <param name="selected_search_scheme" value="GridSearchCV"/>
-            <param name="infile_pipeline" value="pipeline01"/>
+            <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"/>
@@ -279,7 +281,7 @@
         </test>
         <test>
             <param name="selected_search_scheme" value="GridSearchCV"/>
-            <param name="infile_pipeline" value="pipeline06"/>
+            <param name="infile_pipeline" value="pipeline06" ftype="zip"/>
             <conditional name="search_param_selector">
                 <param name="search_p" value="n_estimators: [10, 50, 200, 1000]"/>
                 <param name="selected_param_type" value="final_estimator_p"/>
@@ -303,7 +305,7 @@
         </test>
         <test>
             <param name="selected_search_scheme" value="GridSearchCV"/>
-            <param name="infile_pipeline" value="pipeline07"/>
+            <param name="infile_pipeline" value="pipeline07" ftype="zip"/>
             <conditional name="search_param_selector">
                 <param name="search_p" value="n_estimators: [10, 50, 100, 200]"/>
                 <param name="selected_param_type" value="final_estimator_p"/>
@@ -331,7 +333,7 @@
         </test>
         <test>
             <param name="selected_search_scheme" value="GridSearchCV"/>
-            <param name="infile_pipeline" value="pipeline08"/>
+            <param name="infile_pipeline" value="pipeline08" ftype="zip"/>
             <conditional name="search_param_selector">
                 <param name="search_p" value="n_estimators: [10, 50, 100, 200]"/>
                 <param name="selected_param_type" value="final_estimator_p"/>
@@ -358,7 +360,7 @@
         </test>
         <test>
             <param name="selected_search_scheme" value="GridSearchCV"/>
-            <param name="infile_pipeline" value="pipeline01"/>
+            <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"/>
@@ -374,7 +376,7 @@
         </test>
         <test>
             <param name="selected_search_scheme" value="GridSearchCV"/>
-            <param name="infile_pipeline" value="pipeline03"/>
+            <param name="infile_pipeline" value="pipeline03" ftype="zip"/>
             <conditional name="search_param_selector">
                 <param name="search_p" value="n_estimators: [10, 50, 200, 1000]"/>
                 <param name="selected_param_type" value="final_estimator_p"/>
@@ -400,7 +402,7 @@
         </test>
         <test>
             <param name="selected_search_scheme" value="GridSearchCV"/>
-            <param name="infile_pipeline" value="pipeline09"/>
+            <param name="infile_pipeline" value="pipeline09" ftype="zip"/>
             <conditional name="search_param_selector">
                 <param name="search_p" value="n_neighbors: [50, 100, 150, 200]"/>
                 <param name="selected_param_type" value="prep_1_p"/>
@@ -478,5 +480,8 @@
 
         ]]>
     </help>
-    <expand macro="sklearn_citation"/>
+    <expand macro="sklearn_citation">
+        <expand macro="skrebate_citation"/>
+        <expand macro="xgboost_citation"/>
+    </expand>
 </tool>