Mercurial > repos > bgruening > svm_classifier
comparison svm.xml @ 15:eaccbf2c2891 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
author | bgruening |
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date | Fri, 13 Jul 2018 03:54:16 -0400 |
parents | 78c664cc1841 |
children |
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14:973ffe8fe4f1 | 15:eaccbf2c2891 |
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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> |