Mercurial > repos > bgruening > svm_classifier

comparison svm.xml @ 20:8a07bdbe4cdf draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
author bgruening
date Fri, 13 Jul 2018 03:49:05 -0400
parents b70724d5445e
children
comparison
equal deleted inserted replaced
19:f68956780fbc 20:8a07bdbe4cdf
24 24
25 @COLUMNS_FUNCTION@ 25 @COLUMNS_FUNCTION@
26 @GET_X_y_FUNCTION@ 26 @GET_X_y_FUNCTION@
27 27
28 input_json_path = sys.argv[1] 28 input_json_path = sys.argv[1]
29 params = json.load(open(input_json_path, "r")) 29 with open(input_json_path, "r") as param_handler:
30 params = json.load(param_handler)
30 31
31 #if $selected_tasks.selected_task == "load": 32 #if $selected_tasks.selected_task == "load":
32 33
33 classifier_object = pickle.load(open("$infile_model", 'rb')) 34 with open("$infile_model", 'rb') as model_handler:
35 classifier_object = pickle.load(model_handler)
34 36
35 header = 'infer' if params["selected_tasks"]["header"] else None 37 header = 'infer' if params["selected_tasks"]["header"] else None
36 data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=header, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False) 38 data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=header, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False)
37 prediction = classifier_object.predict(data) 39 prediction = classifier_object.predict(data)
38 prediction_df = pandas.DataFrame(prediction) 40 prediction_df = pandas.DataFrame(prediction)
52 54
53 my_class = getattr(sklearn.svm, selected_algorithm) 55 my_class = getattr(sklearn.svm, selected_algorithm)
54 classifier_object = my_class(**options) 56 classifier_object = my_class(**options)
55 classifier_object.fit(X, y) 57 classifier_object.fit(X, y)
56 58
57 pickle.dump(classifier_object,open("$outfile_fit", 'w+')) 59 with open("$outfile_fit", 'wb') as out_handler:
60 pickle.dump(classifier_object, out_handler)
58 61
59 #end if 62 #end if
60 63
61 ]]> 64 ]]>
62 </configfile> 65 </configfile>