Mercurial > repos > bgruening > sklearn_numeric_clustering

annotate simple_model_fit.py @ 36:73e7f1c76ece draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
author bgruening
date Sat, 01 May 2021 00:48:46 +0000
parents e7f047a9dca9
children 06d772036a62
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
1 import argparse
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
2 import json
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
3 import pickle
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
4
35
e7f047a9dca9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 34
diff changeset
5 import pandas as pd
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
6 from galaxy_ml.utils import load_model, read_columns
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
7 from scipy.io import mmread
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
8 from sklearn.pipeline import Pipeline
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
9
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
10 N_JOBS = int(__import__("os").environ.get("GALAXY_SLOTS", 1))
30
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
11
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
12
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
13 # TODO import from galaxy_ml.utils in future versions
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
14 def clean_params(estimator, n_jobs=None):
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
15 """clean unwanted hyperparameter settings
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
16
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
17 If n_jobs is not None, set it into the estimator, if applicable
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
18
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
19 Return
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
20 ------
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
21 Cleaned estimator object
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
22 """
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
23 ALLOWED_CALLBACKS = (
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
24 "EarlyStopping",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
25 "TerminateOnNaN",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
26 "ReduceLROnPlateau",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
27 "CSVLogger",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
28 "None",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
29 )
30
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
30
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
31 estimator_params = estimator.get_params()
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
32
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
33 for name, p in estimator_params.items():
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
34 # all potential unauthorized file write
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
35 if name == "memory" or name.endswith("__memory") or name.endswith("_path"):
30
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
36 new_p = {name: None}
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
37 estimator.set_params(**new_p)
36
73e7f1c76ece "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 35
diff changeset
38 elif n_jobs is not None and (name == "n_jobs" or name.endswith("__n_jobs")):
30
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
39 new_p = {name: n_jobs}
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
40 estimator.set_params(**new_p)
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
41 elif name.endswith("callbacks"):
30
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
42 for cb in p:
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
43 cb_type = cb["callback_selection"]["callback_type"]
30
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
44 if cb_type not in ALLOWED_CALLBACKS:
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
45 raise ValueError("Prohibited callback type: %s!" % cb_type)
30
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
46
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
47 return estimator
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
48
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
49
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
50 def _get_X_y(params, infile1, infile2):
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
51 """read from inputs and output X and y
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
52
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
53 Parameters
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
54 ----------
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
55 params : dict
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
56 Tool inputs parameter
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
57 infile1 : str
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
58 File path to dataset containing features
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
59 infile2 : str
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
60 File path to dataset containing target values
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
61
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
62 """
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
63 # store read dataframe object
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
64 loaded_df = {}
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
65
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
66 input_type = params["input_options"]["selected_input"]
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
67 # tabular input
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
68 if input_type == "tabular":
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
69 header = "infer" if params["input_options"]["header1"] else None
36
73e7f1c76ece "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 35
diff changeset
70 column_option = params["input_options"]["column_selector_options_1"][
73e7f1c76ece "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 35
diff changeset
71 "selected_column_selector_option"
73e7f1c76ece "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 35
diff changeset
72 ]
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
73 if column_option in [
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
74 "by_index_number",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
75 "all_but_by_index_number",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
76 "by_header_name",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
77 "all_but_by_header_name",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
78 ]:
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
79 c = params["input_options"]["column_selector_options_1"]["col1"]
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
80 else:
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
81 c = None
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
82
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
83 df_key = infile1 + repr(header)
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
84 df = pd.read_csv(infile1, sep="\t", header=header, parse_dates=True)
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
85 loaded_df[df_key] = df
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
86
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
87 X = read_columns(df, c=c, c_option=column_option).astype(float)
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
88 # sparse input
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
89 elif input_type == "sparse":
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
90 X = mmread(open(infile1, "r"))
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
91
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
92 # Get target y
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
93 header = "infer" if params["input_options"]["header2"] else None
36
73e7f1c76ece "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 35
diff changeset
94 column_option = params["input_options"]["column_selector_options_2"][
73e7f1c76ece "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 35
diff changeset
95 "selected_column_selector_option2"
73e7f1c76ece "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 35
diff changeset
96 ]
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
97 if column_option in [
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
98 "by_index_number",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
99 "all_but_by_index_number",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
100 "by_header_name",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
101 "all_but_by_header_name",
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
102 ]:
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
103 c = params["input_options"]["column_selector_options_2"]["col2"]
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
104 else:
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
105 c = None
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
106
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
107 df_key = infile2 + repr(header)
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
108 if df_key in loaded_df:
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
109 infile2 = loaded_df[df_key]
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
110 else:
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
111 infile2 = pd.read_csv(infile2, sep="\t", header=header, parse_dates=True)
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
112 loaded_df[df_key] = infile2
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
113
36
73e7f1c76ece "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 35
diff changeset
114 y = read_columns(
73e7f1c76ece "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 35
diff changeset
115 infile2, c=c, c_option=column_option, sep="\t", header=header, parse_dates=True
73e7f1c76ece "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 35
diff changeset
116 )
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
117 if len(y.shape) == 2 and y.shape[1] == 1:
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
118 y = y.ravel()
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
119
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
120 return X, y
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
121
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
122
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
123 def main(inputs, infile_estimator, infile1, infile2, out_object, out_weights=None):
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
124 """main
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
125
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
126 Parameters
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
127 ----------
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
128 inputs : str
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
129 File path to galaxy tool parameter
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
130
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
131 infile_estimator : str
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
132 File paths of input estimator
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
133
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
134 infile1 : str
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
135 File path to dataset containing features
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
136
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
137 infile2 : str
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
138 File path to dataset containing target labels
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
139
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
140 out_object : str
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
141 File path for output of fitted model or skeleton
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
142
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
143 out_weights : str
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
144 File path for output of weights
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
145
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
146 """
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
147 with open(inputs, "r") as param_handler:
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
148 params = json.load(param_handler)
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
149
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
150 # load model
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
151 with open(infile_estimator, "rb") as est_handler:
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
152 estimator = load_model(est_handler)
30
772db6f8bc24 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
parents: 29
diff changeset
153 estimator = clean_params(estimator, n_jobs=N_JOBS)
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
154
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
155 X_train, y_train = _get_X_y(params, infile1, infile2)
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
156
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
157 estimator.fit(X_train, y_train)
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
158
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
159 main_est = estimator
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
160 if isinstance(main_est, Pipeline):
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
161 main_est = main_est.steps[-1][-1]
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
162 if hasattr(main_est, "model_") and hasattr(main_est, "save_weights"):
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
163 if out_weights:
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
164 main_est.save_weights(out_weights)
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
165 del main_est.model_
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
166 del main_est.fit_params
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
167 del main_est.model_class_
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
168 if getattr(main_est, "validation_data", None):
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
169 del main_est.validation_data
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
170 if getattr(main_est, "data_generator_", None):
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
171 del main_est.data_generator_
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
172
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
173 with open(out_object, "wb") as output_handler:
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
174 pickle.dump(estimator, output_handler, pickle.HIGHEST_PROTOCOL)
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
175
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
176
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
177 if __name__ == "__main__":
29
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
178 aparser = argparse.ArgumentParser()
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
179 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
180 aparser.add_argument("-X", "--infile_estimator", dest="infile_estimator")
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
181 aparser.add_argument("-y", "--infile1", dest="infile1")
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
182 aparser.add_argument("-g", "--infile2", dest="infile2")
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
183 aparser.add_argument("-o", "--out_object", dest="out_object")
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
184 aparser.add_argument("-t", "--out_weights", dest="out_weights")
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
185 args = aparser.parse_args()
9ff214ce6ec2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
186
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
187 main(
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
188 args.inputs,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
189 args.infile_estimator,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
190 args.infile1,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
191 args.infile2,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
192 args.out_object,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
193 args.out_weights,
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 30
diff changeset
194 )