Mercurial > repos > bgruening > sklearn_ensemble

annotate ensemble.xml @ 44:1682df52c084 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 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
author bgruening
date Fri, 22 Sep 2023 17:19:09 +0000
parents 6546d7c9f08b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
41
6546d7c9f08b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 35
diff changeset
1 <tool id="sklearn_ensemble" name="Ensemble methods" version="@VERSION@" profile="@PROFILE@">
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
2 <description>for classification and regression</description>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
3 <macros>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
4 <import>main_macros.xml</import>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
5 </macros>
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
6 <expand macro="python_requirements" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
7 <expand macro="macro_stdio" />
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
8 <version_command>echo "@VERSION@"</version_command>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
9 <command><![CDATA[
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
10 python "$ensemble_script" '$inputs'
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
11 ]]>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
12 </command>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
13 <configfiles>
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
14 <inputs name="inputs" />
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
15 <configfile name="ensemble_script">
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
16 <![CDATA[
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
17 import json
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
18 import numpy as np
24
e94395c672bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 23
diff changeset
19 import pandas
26
dde0f1654d18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
20 import sys
dde0f1654d18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
21
24
e94395c672bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 23
diff changeset
22 from scipy.io import mmread
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
23 import sklearn.ensemble
41
6546d7c9f08b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 35
diff changeset
24 from galaxy_ml.model_persist import dump_model_to_h5, load_model_from_h5
6546d7c9f08b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 35
diff changeset
25 from galaxy_ml.utils import clean_params, get_X_y
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
26
24
e94395c672bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 23
diff changeset
27
e94395c672bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 23
diff changeset
28 N_JOBS = int(__import__('os').environ.get('GALAXY_SLOTS', 1))
4
0431274c367d planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit cea052cf3b8dd4f3620253bd222e126de32e7466
bgruening
parents: 2
diff changeset
29
14
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
30 # Get inputs, outputs.
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
31 input_json_path = sys.argv[1]
15
f02eeabab5d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 14
diff changeset
32 with open(input_json_path, "r") as param_handler:
f02eeabab5d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 14
diff changeset
33 params = json.load(param_handler)
f02eeabab5d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 14
diff changeset
34 print(params)
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
35
14
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
36 # Put all cheetah up here to avoid confusion.
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
37 #if $selected_tasks.selected_task == "train":
14
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
38 infile1 = "$selected_tasks.selected_algorithms.input_options.infile1"
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
39 infile2 = "$selected_tasks.selected_algorithms.input_options.infile2"
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
40 #else:
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
41 infile_model = "$selected_tasks.infile_model"
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
42 infile_data = "$selected_tasks.infile_data"
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
43 #end if
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
44 outfile_fit = "$outfile_fit"
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
45 outfile_predict = "$outfile_predict"
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
46
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
47 # All Python from here on out:
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
48
14
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
49 if params["selected_tasks"]["selected_task"] == "train":
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
50 algorithm = params["selected_tasks"]["selected_algorithms"]["selected_algorithm"]
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
51 options = params["selected_tasks"]["selected_algorithms"]["options"]
19
4570575d060c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 15
diff changeset
52 if algorithm in ['RandomForestClassifier', 'RandomForestRegressor']:
4570575d060c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 15
diff changeset
53 options['n_jobs'] = N_JOBS
14
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
54 if "select_max_features" in options:
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
55 if options["select_max_features"]["max_features"] == "number_input":
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
56 options["select_max_features"]["max_features"] = options["select_max_features"]["num_max_features"]
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
57 options["select_max_features"].pop("num_max_features")
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
58 options["max_features"] = options["select_max_features"]["max_features"]
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
59 options.pop("select_max_features")
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
60 if "min_samples_leaf" in options and options["min_samples_leaf"] == 1.0:
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
61 options["min_samples_leaf"] = 1
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
62 if "min_samples_split" in options and options["min_samples_split"] > 1.0:
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
63 options["min_samples_split"] = int(options["min_samples_split"])
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
64
14
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
65 X, y = get_X_y(params, infile1, infile2)
15
f02eeabab5d1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
bgruening
parents: 14
diff changeset
66
14
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
67 my_class = getattr(sklearn.ensemble, algorithm)
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
68 estimator = my_class(**options)
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
69 estimator.fit(X,y)
41
6546d7c9f08b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 35
diff changeset
70 dump_model_to_h5(estimator, outfile_fit)
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
71
14
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
72 else:
41
6546d7c9f08b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 35
diff changeset
73 classifier_object = load_model_from_h5(infile_model)
6546d7c9f08b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 35
diff changeset
74 classifier_object = clean_params(classifier_object)
14
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
75 header = 'infer' if params["selected_tasks"]["header"] else None
31
af0523c606a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 26
diff changeset
76 data = pandas.read_csv(infile_data, sep='\t', header=header, index_col=None, parse_dates=True, encoding=None)
14
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
77 prediction = classifier_object.predict(data)
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
78 prediction_df = pandas.DataFrame(prediction, columns=["predicted"])
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
79 res = pandas.concat([data, prediction_df], axis=1)
84724d805bfa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 13
diff changeset
80 res.to_csv(path_or_buf = outfile_predict, sep="\t", index=False)
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
81
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
82 ]]>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
83 </configfile>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
84 </configfiles>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
85 <inputs>
41
6546d7c9f08b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 35
diff changeset
86 <expand macro="sl_Conditional" model="h5mlm">
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
87 <param name="selected_algorithm" type="select" label="Select an ensemble method:">
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
88 <option value="RandomForestClassifier" selected="true">Random forest classifier</option>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
89 <option value="AdaBoostClassifier">Ada boost classifier</option>
5
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
90 <option value="GradientBoostingClassifier">Gradient Boosting Classifier</option>
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
91 <option value="RandomForestRegressor">Random forest regressor</option>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
92 <option value="AdaBoostRegressor">Ada boost regressor</option>
5
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
93 <option value="GradientBoostingRegressor">Gradient Boosting Regressor</option>
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
94 </param>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
95 <when value="RandomForestClassifier">
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
96 <expand macro="sl_mixed_input" />
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
97 <section name="options" title="Advanced Options" expanded="False">
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
98 <expand macro="n_estimators" default_value="100" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
99 <expand macro="criterion" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
100 <expand macro="max_features" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
101 <expand macro="max_depth" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
102 <expand macro="min_samples_split" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
103 <expand macro="min_samples_leaf" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
104 <expand macro="min_weight_fraction_leaf" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
105 <expand macro="max_leaf_nodes" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
106 <expand macro="bootstrap" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
107 <expand macro="warm_start" checked="false" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
108 <expand macro="random_state" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
109 <expand macro="oob_score" />
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
110 <!--class_weight=None-->
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
111 </section>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
112 </when>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
113 <when value="AdaBoostClassifier">
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
114 <expand macro="sl_mixed_input" />
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
115 <section name="options" title="Advanced Options" expanded="False">
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
116 <!--base_estimator=None-->
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
117 <expand macro="n_estimators" default_value="50" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
118 <expand macro="learning_rate" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
119 <param argument="algorithm" type="select" label="Boosting algorithm" help=" ">
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
120 <option value="SAMME.R" selected="true">SAMME.R</option>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
121 <option value="SAMME">SAMME</option>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
122 </param>
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
123 <expand macro="random_state" />
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
124 </section>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
125 </when>
5
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
126 <when value="GradientBoostingClassifier">
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
127 <expand macro="sl_mixed_input" />
5
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
128 <section name="options" title="Advanced Options" expanded="False">
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
129 <!--base_estimator=None-->
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
130 <param argument="loss" type="select" label="Loss function">
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
131 <option value="deviance" selected="true">deviance - logistic regression with probabilistic outputs</option>
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
132 <option value="exponential">exponential - gradient boosting recovers the AdaBoost algorithm</option>
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
133 </param>
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
134 <expand macro="learning_rate" default_value='0.1' />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
135 <expand macro="n_estimators" default_value="100" help="The number of boosting stages to perform" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
136 <expand macro="max_depth" default_value="3" help="maximum depth of the individual regression estimators" />
5
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
137 <expand macro="criterion2">
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
138 <option value="friedman_mse" selected="true">friedman_mse - mean squared error with improvement score by Friedman</option>
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
139 </expand>
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
140 <expand macro="min_samples_split" type="float" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
141 <expand macro="min_samples_leaf" type="float" label="The minimum number of samples required to be at a leaf node" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
142 <expand macro="min_weight_fraction_leaf" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
143 <expand macro="subsample" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
144 <expand macro="max_features" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
145 <expand macro="max_leaf_nodes" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
146 <expand macro="min_impurity_decrease" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
147 <expand macro="verbose" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
148 <expand macro="warm_start" checked="false" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
149 <expand macro="random_state" />
5
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
150 </section>
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
151 </when>
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
152 <when value="RandomForestRegressor">
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
153 <expand macro="sl_mixed_input" />
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
154 <section name="options" title="Advanced Options" expanded="False">
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
155 <expand macro="n_estimators" default_value="100" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
156 <expand macro="criterion2" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
157 <expand macro="max_features" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
158 <expand macro="max_depth" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
159 <expand macro="min_samples_split" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
160 <expand macro="min_samples_leaf" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
161 <expand macro="min_weight_fraction_leaf" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
162 <expand macro="max_leaf_nodes" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
163 <expand macro="min_impurity_decrease" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
164 <expand macro="bootstrap" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
165 <expand macro="oob_score" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
166 <expand macro="random_state" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
167 <expand macro="verbose" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
168 <expand macro="warm_start" checked="false" />
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
169 </section>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
170 </when>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
171 <when value="AdaBoostRegressor">
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
172 <expand macro="sl_mixed_input" />
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
173 <section name="options" title="Advanced Options" expanded="False">
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
174 <!--base_estimator=None-->
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
175 <expand macro="n_estimators" default_value="50" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
176 <expand macro="learning_rate" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
177 <param argument="loss" type="select" label="Loss function" optional="true" help="Used when updating the weights after each boosting iteration. ">
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
178 <option value="linear" selected="true">linear</option>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
179 <option value="square">square</option>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
180 <option value="exponential">exponential</option>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
181 </param>
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
182 <expand macro="random_state" />
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
183 </section>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
184 </when>
5
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
185 <when value="GradientBoostingRegressor">
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
186 <expand macro="sl_mixed_input" />
5
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
187 <section name="options" title="Advanced Options" expanded="False">
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
188 <param argument="loss" type="select" label="Loss function">
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
189 <option value="ls" selected="true">ls - least squares regression</option>
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
190 <option value="lad">lad - least absolute deviation</option>
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
191 <option value="huber">huber - combination of least squares regression and least absolute deviation</option>
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
192 <option value="quantile">quantile - use alpha to specify the quantile</option>
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
193 </param>
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
194 <expand macro="learning_rate" default_value="0.1" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
195 <expand macro="n_estimators" default_value="100" help="The number of boosting stages to perform" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
196 <expand macro="max_depth" default_value="3" help="maximum depth of the individual regression estimators" />
5
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
197 <expand macro="criterion2">
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
198 <option value="friedman_mse" selected="true">friedman_mse - mean squared error with improvement score by Friedman</option>
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
199 </expand>
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
200 <expand macro="min_samples_split" type="float" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
201 <expand macro="min_samples_leaf" type="float" label="The minimum number of samples required to be at a leaf node" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
202 <expand macro="min_weight_fraction_leaf" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
203 <expand macro="subsample" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
204 <expand macro="max_features" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
205 <expand macro="max_leaf_nodes" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
206 <expand macro="min_impurity_decrease" />
5
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
207 <param argument="alpha" type="float" value="0.9" label="alpha" help="The alpha-quantile of the huber loss function and the quantile loss function" />
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
208 <!--base_estimator=None-->
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
209 <expand macro="verbose" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
210 <expand macro="warm_start" checked="false" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
211 <expand macro="random_state" />
5
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
212 </section>
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
213 </when>
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
214 </expand>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
215 </inputs>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
216
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
217 <expand macro="output" />
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
218
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
219 <tests>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
220 <test>
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
221 <param name="infile1" value="train.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
222 <param name="infile2" value="train.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
223 <param name="col1" value="1,2,3,4" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
224 <param name="col2" value="5" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
225 <param name="selected_task" value="train" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
226 <param name="selected_algorithm" value="RandomForestClassifier" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
227 <param name="random_state" value="10" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
228 <output name="outfile_fit" file="rfc_model01" compare="sim_size" delta="5" />
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
229 </test>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
230 <test>
41
6546d7c9f08b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 35
diff changeset
231 <param name="infile_model" value="rfc_model01" ftype="h5mlm" />
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
232 <param name="infile_data" value="test.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
233 <param name="selected_task" value="load" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
234 <output name="outfile_predict" file="rfc_result01" />
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
235 </test>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
236 <test>
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
237 <param name="infile1" value="regression_train.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
238 <param name="infile2" value="regression_train.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
239 <param name="col1" value="1,2,3,4,5" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
240 <param name="col2" value="6" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
241 <param name="selected_task" value="train" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
242 <param name="selected_algorithm" value="RandomForestRegressor" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
243 <param name="random_state" value="10" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
244 <output name="outfile_fit" file="rfr_model01" compare="sim_size" delta="5" />
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
245 </test>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
246 <test>
41
6546d7c9f08b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 35
diff changeset
247 <param name="infile_model" value="rfr_model01" ftype="h5mlm" />
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
248 <param name="infile_data" value="regression_test.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
249 <param name="selected_task" value="load" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
250 <output name="outfile_predict" file="rfr_result01" />
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
251 </test>
5
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
252 <test>
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
253 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
254 <param name="infile2" value="regression_y.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
255 <param name="header1" value="True" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
256 <param name="selected_column_selector_option" value="all_columns" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
257 <param name="header2" value="True" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
258 <param name="col2" value="1" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
259 <param name="selected_task" value="train" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
260 <param name="selected_algorithm" value="GradientBoostingRegressor" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
261 <param name="max_features" value="number_input" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
262 <param name="num_max_features" value="0.5" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
263 <param name="random_state" value="42" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
264 <output name="outfile_fit" file="gbr_model01" compare="sim_size" delta="5" />
5
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
265 </test>
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
266 <test>
41
6546d7c9f08b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 35
diff changeset
267 <param name="infile_model" value="gbr_model01" ftype="h5mlm" />
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
268 <param name="infile_data" value="regression_test_X.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
269 <param name="selected_task" value="load" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
270 <param name="header" value="True" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
271 <output name="outfile_predict" file="gbr_prediction_result01.tabular" />
5
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
272 </test>
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
273 <test>
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
274 <param name="infile1" value="train.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
275 <param name="infile2" value="train.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
276 <param name="col1" value="1,2,3,4" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
277 <param name="col2" value="5" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
278 <param name="selected_task" value="train" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
279 <param name="selected_algorithm" value="GradientBoostingClassifier" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
280 <output name="outfile_fit" file="gbc_model01" compare="sim_size" delta="5" />
5
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
281 </test>
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
282 <test>
41
6546d7c9f08b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 35
diff changeset
283 <param name="infile_model" value="gbc_model01" ftype="h5mlm" />
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
284 <param name="infile_data" value="test.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
285 <param name="selected_task" value="load" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
286 <output name="outfile_predict" file="gbc_result01" />
5
f1761288587e planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 4
diff changeset
287 </test>
22
2e69c6ca6e91 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 21
diff changeset
288 <test>
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
289 <param name="infile1" value="train.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
290 <param name="infile2" value="train.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
291 <param name="col1" value="1,2,3,4" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
292 <param name="col2" value="5" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
293 <param name="selected_task" value="train" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
294 <param name="selected_algorithm" value="AdaBoostClassifier" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
295 <param name="random_state" value="10" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
296 <output name="outfile_fit" file="abc_model01" compare="sim_size" delta="5" />
22
2e69c6ca6e91 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 21
diff changeset
297 </test>
2e69c6ca6e91 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 21
diff changeset
298 <test>
41
6546d7c9f08b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 35
diff changeset
299 <param name="infile_model" value="abc_model01" ftype="h5mlm" />
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
300 <param name="infile_data" value="test.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
301 <param name="selected_task" value="load" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
302 <output name="outfile_predict" file="abc_result01" />
22
2e69c6ca6e91 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 21
diff changeset
303 </test>
2e69c6ca6e91 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 21
diff changeset
304 <test>
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
305 <param name="infile1" value="regression_train.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
306 <param name="infile2" value="regression_train.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
307 <param name="col1" value="1,2,3,4,5" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
308 <param name="col2" value="6" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
309 <param name="selected_task" value="train" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
310 <param name="selected_algorithm" value="AdaBoostRegressor" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
311 <param name="random_state" value="10" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
312 <output name="outfile_fit" file="abr_model01" compare="sim_size" delta="5" />
22
2e69c6ca6e91 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 21
diff changeset
313 </test>
2e69c6ca6e91 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 21
diff changeset
314 <test>
41
6546d7c9f08b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 35
diff changeset
315 <param name="infile_model" value="abr_model01" ftype="h5mlm" />
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
316 <param name="infile_data" value="regression_test.tabular" ftype="tabular" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
317 <param name="selected_task" value="load" />
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
318 <output name="outfile_predict" file="abr_result01" />
22
2e69c6ca6e91 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
bgruening
parents: 21
diff changeset
319 </test>
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
320 </tests>
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
321 <help><![CDATA[
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
322 ***What it does***
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
323 The goal of ensemble methods is to combine the predictions of several base estimators built with a given learning algorithm in order to improve generalizability / robustness over a single estimator. This tool offers two sets of ensemble algorithms for classification and regression: random forests and ADA boosting which are based on sklearn.ensemble library from Scikit-learn. Here you can find out about the input, output and methods presented in the tools. For information about ensemble methods and parameters settings please refer to `Scikit-learn ensemble`_.
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
324
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
325 .. _`Scikit-learn ensemble`: http://scikit-learn.org/stable/modules/ensemble.html
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
326
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
327 **1 - Methods**
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
328 There are two groups of operations available:
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
329
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
330 1 - Train a model : A training set containing samples and their respective labels (or predicted values) are input. Based on the selected algorithm and options, an estimator object is fit to the data and is returned.
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
331
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
332 2 - Load a model and predict : An existing model predicts the class labels (or regression values) for a new dataset.
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
333
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
334 **2 - Trainig input**
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
335 When you choose to train a model, you need a features dataset X and a labels set y. This tool expects tabular or sparse data for X and a single column for y (tabular). You can select a subset of columns in a tabular dataset as your features dataset or labels column. Below you find some examples:
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
336
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
337 **Sample tabular features dataset**
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
338 The following training dataset contains 3 feature columns and a column containing class labels. You can simply select the first 3 columns as features and the last column as labels:
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
339
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
340 ::
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
341
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
342 4.01163365529 -6.10797684314 8.29829894763 1
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
343 10.0788438916 1.59539821454 10.0684278289 0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
344 -5.17607775503 -0.878286135332 6.92941850665 2
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
345 4.00975406235 -7.11847496542 9.3802423585 1
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
346 4.61204065139 -5.71217537352 9.12509610964 1
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
347
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
348
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
349 **Sample sparse features dataset**
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
350 In this case you cannot specifiy a column range.
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
351
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
352 ::
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
353
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
354 4 1048577 8738
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
355 1 271 0.02083333333333341
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
356 1 1038 0.02461995616119806
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
357 2 829017 0.01629088031127686
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
358 2 829437 0.01209127083516686
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
359 2 830752 0.02535100632816968
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
360 3 1047487 0.01485722929945572
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
361 3 1047980 0.02640566620767753
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
362 3 1048475 0.01665869913262564
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
363 4 608 0.01662975263094352
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
364 4 1651 0.02519674277562741
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
365 4 4053 0.04223659971350601
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
366
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
367
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
368 **2 - Trainig output**
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
369 The trained model is generated and output in the form of a binary file.
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
370
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
371
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
372 **3 - Prediction input**
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
373
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
374 When you choose to load a model and do prediction, the tool expects an already trained estimator and a tabular dataset as input. The dataset contains new samples which you want to classify or predict regression values for.
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
375
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
376
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
377 .. class:: warningmark
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
378
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
379 The number of feature columns must be the same in training and prediction datasets!
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
380
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
381
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
382 **3 - Prediction output**
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
383 The tool predicts the class labels for new samples and adds them as the last column to the prediction dataset. The new dataset then is output as a tabular file. The prediction output format should look like the training dataset.
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
384
35
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
385 ]]> </help>
19d6c2745d34 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
386 <expand macro="sklearn_citation" />
0
569eefee7ed8 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
387 </tool>