Mercurial > repos > bgruening > sklearn_ensemble

comparison ensemble.xml @ 8:ea8b1c89c20b draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit cea052cf3b8dd4f3620253bd222e126de32e7466
author bgruening
date Thu, 22 Mar 2018 13:43:19 -0400
parents 4c2fae2db5d1
children e4fcbbc81083
comparison
equal deleted inserted replaced
7:237975a3f472 8:ea8b1c89c20b
20 import sklearn.ensemble 20 import sklearn.ensemble
21 import pandas 21 import pandas
22 import pickle 22 import pickle
23 from scipy.io import mmread 23 from scipy.io import mmread
24 24
25 @COLUMNS_FUNCTION@
26
25 input_json_path = sys.argv[1] 27 input_json_path = sys.argv[1]
26 params = json.load(open(input_json_path, "r")) 28 params = json.load(open(input_json_path, "r"))
27
28 @COLUMNS_FUNCTION@
29 29
30 #if $selected_tasks.selected_task == "train": 30 #if $selected_tasks.selected_task == "train":
31 31
32 algorithm = params["selected_tasks"]["selected_algorithms"]["selected_algorithm"] 32 algorithm = params["selected_tasks"]["selected_algorithms"]["selected_algorithm"]
33 options = params["selected_tasks"]["selected_algorithms"]["options"] 33 options = params["selected_tasks"]["selected_algorithms"]["options"]
34 input_type = params["selected_tasks"]["selected_algorithms"]["input_options"]["selected_input"] 34 input_type = params["selected_tasks"]["selected_algorithms"]["input_options"]["selected_input"]
35 if input_type=="tabular": 35 if input_type=="tabular":
36 header = 'infer' if params["selected_tasks"]["selected_algorithms"]["input_options"]["header1"] else None
36 X = read_columns( 37 X = read_columns(
37 "$selected_tasks.selected_algorithms.input_options.infile1", 38 "$selected_tasks.selected_algorithms.input_options.infile1",
38 "$selected_tasks.selected_algorithms.input_options.col1", 39 "$selected_tasks.selected_algorithms.input_options.col1",
39 sep='\t', 40 sep='\t',
40 header=None, 41 header=header,
41 parse_dates=True 42 parse_dates=True
42 ) 43 )
43 else: 44 else:
44 X = mmread(open("$selected_tasks.selected_algorithms.input_options.infile1", 'r')) 45 X = mmread(open("$selected_tasks.selected_algorithms.input_options.infile1", 'r'))
45 46
47 header = 'infer' if params["selected_tasks"]["selected_algorithms"]["input_options"]["header2"] else None
46 y = read_columns( 48 y = read_columns(
47 "$selected_tasks.selected_algorithms.input_options.infile2", 49 "$selected_tasks.selected_algorithms.input_options.infile2",
48 "$selected_tasks.selected_algorithms.input_options.col2", 50 "$selected_tasks.selected_algorithms.input_options.col2",
49 sep='\t', 51 sep='\t',
50 header=None, 52 header=header,
51 parse_dates=True 53 parse_dates=True
52 ) 54 )
53 55
54 my_class = getattr(sklearn.ensemble, algorithm) 56 my_class = getattr(sklearn.ensemble, algorithm)
55 estimator = my_class(**options) 57 estimator = my_class(**options)