diff ensemble.xml @ 13:6352834b1c99 draft

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

--- a/ensemble.xml	Sun Jul 01 03:19:54 2018 -0400
+++ b/ensemble.xml	Mon Jul 09 14:32:15 2018 -0400
@@ -23,6 +23,7 @@
 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"))
@@ -46,40 +47,8 @@
     options["min_samples_leaf"] = 1
 if "min_samples_split" in options and options["min_samples_split"] > 1.0:
     options["min_samples_split"] = int(options["min_samples_split"])
-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(
-            "$selected_tasks.selected_algorithms.input_options.infile1",
-            c = c,
-            c_option = column_option,
-            sep='\t',
-            header=header,
-            parse_dates=True
-    )
-else:
-    X = mmread(open("$selected_tasks.selected_algorithms.input_options.infile1", 'r'))
 
-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(
-        "$selected_tasks.selected_algorithms.input_options.infile2",
-        c = c,
-        c_option = column_option,
-        sep='\t',
-        header=header,
-        parse_dates=True
-)
-y=y.ravel()
+X, y = get_X_y(params, "$selected_tasks.selected_algorithms.input_options.infile1" ,"$selected_tasks.selected_algorithms.input_options.infile2")
 
 my_class = getattr(sklearn.ensemble, algorithm)
 estimator = my_class(**options)