diff generalized_linear.xml @ 13:af9385cae623 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364

--- a/generalized_linear.xml	Sun Jul 01 03:17:30 2018 -0400
+++ b/generalized_linear.xml	Mon Jul 09 14:29:40 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)