Mercurial > repos > bgruening > sklearn_ensemble
comparison ensemble.xml @ 4:0431274c367d draft
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit cea052cf3b8dd4f3620253bd222e126de32e7466
| author | bgruening |
|---|---|
| date | Thu, 22 Mar 2018 13:46:46 -0400 |
| parents | 6e6726be0728 |
| children | f1761288587e |
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| 3:968863bd9008 | 4:0431274c367d |
|---|---|
| 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) |