| Previous changeset 12:513405ebad8b (2018-07-01) Next changeset 14:10a8543142fc (2018-07-10) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364 |
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modified:
generalized_linear.xml main_macros.xml |
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| diff -r 513405ebad8b -r cf635edf37d2 generalized_linear.xml --- a/generalized_linear.xml Sun Jul 01 03:21:11 2018 -0400 +++ b/generalized_linear.xml Mon Jul 09 14:33:39 2018 -0400 |
| [ |
| @@ -23,49 +23,18 @@ from scipy.io import mmread @COLUMNS_FUNCTION@ +@GET_X_y_FUNCTION@ input_json_path = sys.argv[1] params = json.load(open(input_json_path, "r")) #if $selected_tasks.selected_task == "train": +X, y = get_X_y(params, "$selected_tasks.selected_algorithms.input_options.infile1" ,"$selected_tasks.selected_algorithms.input_options.infile2") + algorithm = params["selected_tasks"]["selected_algorithms"]["selected_algorithm"] options = params["selected_tasks"]["selected_algorithms"]["options"] -#if $selected_tasks.selected_algorithms.input_options.selected_input=="tabular": -header = 'infer' if params["selected_tasks"]["selected_algorithms"]["input_options"]["header1"] else None -column_option = params["selected_tasks"]["selected_algorithms"]["input_options"]["column_selector_options_1"]["selected_column_selector_option"] -if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]: - c = params["selected_tasks"]["selected_algorithms"]["input_options"]["column_selector_options_1"]["col1"] -else: - c = None -X = read_columns( - "$selected_tasks.selected_algorithms.input_options.infile1", - c = c, - c_option = column_option, - sep='\t', - header=header, - parse_dates=True -) -#else: -X = mmread(open("$selected_tasks.selected_algorithms.input_options.infile1", 'r')) -#end if - -header = 'infer' if params["selected_tasks"]["selected_algorithms"]["input_options"]["header2"] else None -column_option = params["selected_tasks"]["selected_algorithms"]["input_options"]["column_selector_options_2"]["selected_column_selector_option2"] -if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]: - c = params["selected_tasks"]["selected_algorithms"]["input_options"]["column_selector_options_2"]["col2"] -else: - c = None -y = read_columns( - "$selected_tasks.selected_algorithms.input_options.infile2", - c = c, - c_option = column_option, - sep='\t', - header=header, - parse_dates=True -) - my_class = getattr(sklearn.linear_model, algorithm) estimator = my_class(**options) estimator.fit(X,y) |
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| diff -r 513405ebad8b -r cf635edf37d2 main_macros.xml --- a/main_macros.xml Sun Jul 01 03:21:11 2018 -0400 +++ b/main_macros.xml Mon Jul 09 14:33:39 2018 -0400 |
| [ |
| @@ -64,6 +64,45 @@ return new_selector </token> + <token name="@GET_X_y_FUNCTION@"> +def get_X_y(params, file1, file2): + input_type = params["selected_tasks"]["selected_algorithms"]["input_options"]["selected_input"] + if input_type=="tabular": + header = 'infer' if params["selected_tasks"]["selected_algorithms"]["input_options"]["header1"] else None + column_option = params["selected_tasks"]["selected_algorithms"]["input_options"]["column_selector_options_1"]["selected_column_selector_option"] + if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]: + c = params["selected_tasks"]["selected_algorithms"]["input_options"]["column_selector_options_1"]["col1"] + else: + c = None + X = read_columns( + file1, + c = c, + c_option = column_option, + sep='\t', + header=header, + parse_dates=True + ) + else: + X = mmread(open(file1, 'r')) + + header = 'infer' if params["selected_tasks"]["selected_algorithms"]["input_options"]["header2"] else None + column_option = params["selected_tasks"]["selected_algorithms"]["input_options"]["column_selector_options_2"]["selected_column_selector_option2"] + if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]: + c = params["selected_tasks"]["selected_algorithms"]["input_options"]["column_selector_options_2"]["col2"] + else: + c = None + y = read_columns( + file2, + c = c, + c_option = column_option, + sep='\t', + header=header, + parse_dates=True + ) + y=y.ravel() + return X, y + </token> + <xml name="python_requirements"> <requirements> <requirement type="package" version="2.7">python</requirement> @@ -81,34 +120,6 @@ <!--Generic interface--> - <xml name="train_loadConditional" token_train="tabular" token_data="tabular" token_model="txt"> - <conditional name="selected_tasks"> - <param name="selected_task" type="select" label="Select a Classification Task"> - <option value="train" selected="true">Train a model</option> - <option value="load">Load a model and predict</option> - </param> - <when value="load"> - <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/> - <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/> - <conditional name="prediction_options"> - <param name="prediction_option" type="select" label="Select the type of prediction"> - <option value="predict">Predict class labels</option> - <option value="advanced">Include advanced options</option> - </param> - <when value="predict"> - </when> - <when value="advanced"> - </when> - </conditional> - </when> - <when value="train"> - <param name="infile_train" type="data" format="@TRAIN@" label="Training samples (tabular)"/> - <conditional name="selected_algorithms"> - <yield /> - </conditional> - </when> - </conditional> - </xml> <xml name="sl_Conditional" token_train="tabular" token_data="tabular" token_model="txt"> <conditional name="selected_tasks"> |