Mercurial > repos > bgruening > sklearn_numeric_clustering

comparison numeric_clustering.xml @ 21:89af3ccbec73 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
author bgruening
date Fri, 13 Jul 2018 03:50:30 -0400
parents 60d1b396cea2
children 64200dc3d769
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20:60d1b396cea2 21:89af3ccbec73
23 from scipy.io import mmread 23 from scipy.io import mmread
24 24
25 @COLUMNS_FUNCTION@ 25 @COLUMNS_FUNCTION@
26 26
27 input_json_path = sys.argv[1] 27 input_json_path = sys.argv[1]
28 params = json.load(open(input_json_path, "r")) 28 with open(input_json_path, "r") as param_handler:
29 params = json.load(param_handler)
30
29 31
30 selected_algorithm = params["input_types"]["algorithm_options"]["selected_algorithm"] 32 selected_algorithm = params["input_types"]["algorithm_options"]["selected_algorithm"]
31 33
32 my_class = getattr(sklearn.cluster, selected_algorithm) 34 my_class = getattr(sklearn.cluster, selected_algorithm)
33 cluster_object = my_class() 35 cluster_object = my_class()
34 options = params["input_types"]["algorithm_options"]["options"] 36 options = params["input_types"]["algorithm_options"]["options"]
35 37
36 cluster_object.set_params(**options) 38 cluster_object.set_params(**options)
37 39
38 #if $input_types.selected_input_type == "sparse": 40 #if $input_types.selected_input_type == "sparse":
39 data_matrix = mmread(open("$infile", 'r')) 41 data_matrix = mmread("$infile")
40 #else: 42 #else:
41 data = pandas.read_csv("$infile", sep='\t', header=0, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False ) 43 data = pandas.read_csv("$infile", sep='\t', header=0, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False )
42 header = 'infer' if params["input_types"]["header"] else None 44 header = 'infer' if params["input_types"]["header"] else None
43 column_option = params["input_types"]["column_selector_options"]["selected_column_selector_option"] 45 column_option = params["input_types"]["column_selector_options"]["selected_column_selector_option"]
44 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]: 46 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]: