Mercurial > repos > bgruening > sklearn_svm_classifier
diff svm.xml @ 4:41d0edb7d1fc draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
author | bgruening |
---|---|
date | Thu, 23 Aug 2018 16:14:13 -0400 |
parents | 297541cc26d0 |
children | 1c5989b930e3 |
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--- a/svm.xml Fri Aug 17 12:26:01 2018 -0400 +++ b/svm.xml Thu Aug 23 16:14:13 2018 -0400 @@ -19,9 +19,9 @@ import json import sklearn.svm import pandas -import pickle -execfile("$__tool_directory__/utils.py") +execfile("$__tool_directory__/sk_whitelist.py") +execfile("$__tool_directory__/utils.py", globals()) input_json_path = sys.argv[1] with open(input_json_path, "r") as param_handler: @@ -30,7 +30,7 @@ #if $selected_tasks.selected_task == "load": with open("$infile_model", 'rb') as model_handler: - classifier_object = pickle.load(model_handler) + classifier_object = SafePickler.load(model_handler) header = 'infer' if params["selected_tasks"]["header"] else None data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=header, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False) @@ -55,7 +55,7 @@ classifier_object.fit(X, y) with open("$outfile_fit", 'wb') as out_handler: - pickle.dump(classifier_object, out_handler) + pickle.dump(classifier_object, out_handler, pickle.HIGHEST_PROTOCOL) #end if @@ -122,7 +122,7 @@ <param name="selected_task" value="train"/> <param name="selected_algorithm" value="SVC"/> <param name="random_state" value="5"/> - <output name="outfile_fit" file="svc_model01.txt"/> + <output name="outfile_fit" file="svc_model01.txt" compare="sim_size" delta="1"/> </test> <test> <param name="infile1" value="train_set.tabular" ftype="tabular"/> @@ -134,7 +134,7 @@ <param name="selected_task" value="train"/> <param name="selected_algorithm" value="NuSVC"/> <param name="random_state" value="5"/> - <output name="outfile_fit" file="svc_model02.txt"/> + <output name="outfile_fit" file="svc_model02.txt" compare="sim_size" delta="1"/> </test> <test> <param name="infile1" value="train_set.tabular" ftype="tabular"/> @@ -146,24 +146,24 @@ <param name="selected_task" value="train"/> <param name="selected_algorithm" value="LinearSVC"/> <param name="random_state" value="5"/> - <output name="outfile_fit" file="svc_model03.txt"/> + <output name="outfile_fit" file="svc_model03.txt" compare="sim_size" delta="1"/> </test> <test> - <param name="infile_model" value="svc_model01.txt" ftype="txt"/> + <param name="infile_model" value="svc_model01.txt" ftype="zip"/> <param name="infile_data" value="test_set.tabular" ftype="tabular"/> <param name="header" value="True"/> <param name="selected_task" value="load"/> <output name="outfile_predict" file="svc_prediction_result01.tabular"/> </test> <test> - <param name="infile_model" value="svc_model02.txt" ftype="txt"/> + <param name="infile_model" value="svc_model02.txt" ftype="zip"/> <param name="infile_data" value="test_set.tabular" ftype="tabular"/> <param name="header" value="True"/> <param name="selected_task" value="load"/> <output name="outfile_predict" file="svc_prediction_result02.tabular"/> </test> <test> - <param name="infile_model" value="svc_model03.txt" ftype="txt"/> + <param name="infile_model" value="svc_model03.txt" ftype="zip"/> <param name="infile_data" value="test_set.tabular" ftype="tabular"/> <param name="header" value="True"/> <param name="selected_task" value="load"/>