| Previous changeset 14:10a8543142fc (2018-07-10) Next changeset 16:8ccc9b001a88 (2018-08-04) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48 |
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modified:
generalized_linear.xml main_macros.xml |
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removed:
test-data/mv_result07.tabular |
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| diff -r 10a8543142fc -r f0e215cbade3 generalized_linear.xml --- a/generalized_linear.xml Tue Jul 10 03:13:00 2018 -0400 +++ b/generalized_linear.xml Fri Jul 13 03:56:33 2018 -0400 |
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| @@ -26,7 +26,8 @@ @GET_X_y_FUNCTION@ input_json_path = sys.argv[1] -params = json.load(open(input_json_path, "r")) +with open(input_json_path, "r") as param_handler: + params = json.load(param_handler) #if $selected_tasks.selected_task == "train": @@ -38,10 +39,12 @@ my_class = getattr(sklearn.linear_model, algorithm) estimator = my_class(**options) estimator.fit(X,y) -pickle.dump(estimator,open("$outfile_fit", 'w+'), pickle.HIGHEST_PROTOCOL) +with open("$outfile_fit", 'wb') as out_handler: + pickle.dump(estimator, out_handler, pickle.HIGHEST_PROTOCOL) #else: -classifier_object = pickle.load(open("$selected_tasks.infile_model", 'r')) +with open("$selected_tasks.infile_model", 'rb') as model_handler: + classifier_object = pickle.load(model_handler) data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=None, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False ) prediction = classifier_object.predict(data) prediction_df = pandas.DataFrame(prediction, columns=["predicted"]) |
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| diff -r 10a8543142fc -r f0e215cbade3 main_macros.xml --- a/main_macros.xml Tue Jul 10 03:13:00 2018 -0400 +++ b/main_macros.xml Fri Jul 13 03:56:33 2018 -0400 |
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| b'@@ -35,7 +35,8 @@\n if not options[\'threshold\'] or options[\'threshold\'] == \'None\':\n options[\'threshold\'] = None\n if \'extra_estimator\' in inputs and inputs[\'extra_estimator\'][\'has_estimator\'] == \'no_load\':\n- fitted_estimator = pickle.load(open("inputs[\'extra_estimator\'][\'fitted_estimator\']", \'r\'))\n+ with open("inputs[\'extra_estimator\'][\'fitted_estimator\']", \'rb\') as model_handler:\n+ fitted_estimator = pickle.load(model_handler)\n new_selector = selector(fitted_estimator, prefit=True, **options)\n else:\n estimator=inputs["estimator"]\n@@ -83,7 +84,7 @@\n parse_dates=True\n )\n else:\n- X = mmread(open(file1, \'r\'))\n+ X = mmread(file1)\n \n header = \'infer\' if params["selected_tasks"]["selected_algorithms"]["input_options"]["header2"] else None\n column_option = params["selected_tasks"]["selected_algorithms"]["input_options"]["column_selector_options_2"]["selected_column_selector_option2"]\n@@ -432,19 +433,6 @@\n \n \n <!--Data interface-->\n- <xml name="tabular_input">\n- <param name="infile" type="data" format="tabular" label="Data file with numeric values"/>\n- <param name="start_column" type="data_column" data_ref="infile" optional="True" label="Select a subset of data. Start column:" />\n- <param name="end_column" type="data_column" data_ref="infile" optional="True" label="End column:" />\n- </xml>\n-\n- <xml name="sample_cols" token_label1="File containing true class labels:" token_label2="File containing predicted class labels:" token_multiple1="False" token_multiple2="False" token_format1="tabular" token_format2="tabular" token_help1="" token_help2="">\n- <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>\n- <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/>\n- <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/>\n- <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/>\n- <yield/>\n- </xml>\n \n <xml name="samples_tabular" token_multiple1="false" token_multiple2="false">\n <param name="infile1" type="data" format="tabular" label="Training samples dataset:"/>\n@@ -472,13 +460,13 @@\n <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" data_ref="@INFILE@" label="Select target column(s):"/>\n </when>\n <when value="by_header_name">\n- <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="String seperate by colon. For example: target1,target2"/>\n+ <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="Comma-separated string. For example: target1,target2"/>\n </when>\n <when value="all_but_by_index_number">\n <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" data_ref="@INFILE@" label="Select target column(s):"/>\n </when>\n <when value="all_but_by_header_name">\n- <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="String seperate by colon. For example: target1,target2"/>\n+ <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="Comma-separated string. For example: target1,target2"/>\n </when>\n <when value="all_columns">\n </when>\n@@ -553,11 +541,6 @@\n </conditional>\n </xml>\n \n- <xml name="multitype_input" token_format="tabular" token_help="All datasets with tabular format are supporetd.">\n- <param name="infile_transform" type="data" format="@FORMAT@" label="Select a dataset to transform:" help="@HELP@"/>\n- </xml>\n-\n-\n <!--Advanced options-->\n <xml name="nn_advanced_options">\n <section name="options" title="Advanced Options" expanded="False">\n@@ -822,9 +805,17 @@\n </param>\n </xml>\n \n+ <xml name="sparse_preprocessors_ext">\n+ <expand macro="sparse_preprocessors">\n+ <option value="KernelCenterer">Kernel Centerer (Centers a kernel '..b' Options" expanded="False">\n+ <!--feature_range-->\n+ <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"\n+ label="Use a copy of data for precomputing normalization" help=" "/>\n+ </section>\n+ </when>\n+ <when value="PolynomialFeatures">\n+ <section name="options" title="Advanced Options" expanded="False">\n+ <param argument="degree" type="integer" optional="true" value="2" label="The degree of the polynomial features " help=""/>\n+ <param argument="interaction_only" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Produce interaction features only" help="(Features that are products of at most degree distinct input features) "/>\n+ <param argument="include_bias" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Include a bias column" help="Feature in which all polynomial powers are zero "/>\n+ </section>\n+ </when>\n+ <when value="RobustScaler">\n+ <section name="options" title="Advanced Options" expanded="False">\n+ <!--=True, =True, copy=True-->\n+ <param argument="with_centering" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"\n+ label="Center the data before scaling" help=" "/>\n+ <param argument="with_scaling" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"\n+ label="Scale the data to interquartile range" help=" "/>\n+ <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"\n+ label="Use a copy of data for inplace scaling" help=" "/>\n+ </section>\n+ </when>\n+ </expand>\n+ </xml>\n+\n <xml name="estimator_input_no_fit">\n <expand macro="feature_selection_estimator" />\n <conditional name="extra_estimator">\n@@ -892,6 +914,7 @@\n <expand macro="feature_selection_estimator_choices" />\n </conditional>\n </xml>\n+\n <xml name="feature_selection_all">\n <conditional name="feature_selection_algorithms">\n <param name="selected_algorithm" type="select" label="Select a feature selection algorithm">\n@@ -1014,6 +1037,7 @@\n </when-->\n </conditional>\n </xml>\n+\n <xml name="feature_selection_score_function">\n <param argument="score_func" type="select" label="Select a score function">\n <option value="chi2">chi2 - Compute chi-squared stats between each non-negative feature and class</option>\n@@ -1023,6 +1047,7 @@\n <option value="mutual_info_regression">mutual_info_regression - Estimate mutual information for a continuous target variable</option>\n </param>\n </xml>\n+\n <xml name="feature_selection_estimator">\n <param argument="estimator" type="select" label="Select an estimator" help="The base estimator from which the transformer is built.">\n <option value="svm.SVR(kernel="linear")">svm.SVR(kernel="linear")</option>\n@@ -1032,6 +1057,7 @@\n <option value="ensemble.RandomForestRegressor(n_estimators = 1000, random_state = 42)">ensemble.RandomForestRegressor(n_estimators = 1000, random_state = 42)</option>\n </param>\n </xml>\n+\n <xml name="feature_selection_extra_estimator"> \n <param name="has_estimator" type="select" label="Does your estimator on the list above?">\n <option value="yes">Yes, my estimator is on the list</option>\n@@ -1039,6 +1065,7 @@\n <yield/>\n </param>\n </xml>\n+\n <xml name="feature_selection_estimator_choices">\n <when value="yes">\n </when>\n@@ -1047,6 +1074,7 @@\n </when>\n <yield/>\n </xml>\n+\n <xml name="feature_selection_methods">\n <conditional name="select_methods">\n <param name="selected_method" type="select" label="Select an operation">\n' |
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| diff -r 10a8543142fc -r f0e215cbade3 test-data/mv_result07.tabular --- a/test-data/mv_result07.tabular Tue Jul 10 03:13:00 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -0.7824428015300172 |