Mercurial > repos > bgruening > sklearn_ensemble

annotate ensemble.xml @ 18:0070e491573f 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 7c2fd140e89605fe689c39e21d70a400545e38cf
author bgruening
date Tue, 10 Jul 2018 03:06:57 -0400
parents 760a92d0e174
children 128bd4ab2b82
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
1 <tool id="sklearn_ensemble" name="Ensemble methods" version="@VERSION@">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
2 <description>for classification and regression</description>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
3 <macros>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
4 <import>main_macros.xml</import>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
5 </macros>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
6 <expand macro="python_requirements"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
7 <expand macro="macro_stdio"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
8 <version_command>echo "@VERSION@"</version_command>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
9 <command><![CDATA[
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
10 python "$ensemble_script" '$inputs'
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
11 ]]>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
12 </command>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
13 <configfiles>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
14 <inputs name="inputs"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
15 <configfile name="ensemble_script">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
16 <![CDATA[
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
17 import sys
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
18 import json
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
19 import numpy as np
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
20 import sklearn.ensemble
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
21 import pandas
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
22 import pickle
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
23 from scipy.io import mmread
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
24
8
ea8b1c89c20b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit cea052cf3b8dd4f3620253bd222e126de32e7466
bgruening
parents: 6
diff changeset
25 @COLUMNS_FUNCTION@
17
760a92d0e174 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
bgruening
parents: 16
diff changeset
26 @GET_X_y_FUNCTION@
8
ea8b1c89c20b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit cea052cf3b8dd4f3620253bd222e126de32e7466
bgruening
parents: 6
diff changeset
27
18
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
28 # Get inputs, outputs.
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
29 input_json_path = sys.argv[1]
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
30 params = json.load(open(input_json_path, "r"))
18
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
31 print params
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
32
18
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
33 # Put all cheetah up here to avoid confusion.
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
34 #if $selected_tasks.selected_task == "train":
18
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
35 infile1 = "$selected_tasks.selected_algorithms.input_options.infile1"
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
36 infile2 = "$selected_tasks.selected_algorithms.input_options.infile2"
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
37 #else:
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
38 infile_model = "$selected_tasks.infile_model"
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
39 infile_data = "$selected_tasks.infile_data"
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
40 #end if
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
41 outfile_fit = "$outfile_fit"
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
42 outfile_predict = "$outfile_predict"
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
43
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
44 # All Python from here on out:
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
45
18
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
46 if params["selected_tasks"]["selected_task"] == "train":
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
47 algorithm = params["selected_tasks"]["selected_algorithms"]["selected_algorithm"]
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
48 options = params["selected_tasks"]["selected_algorithms"]["options"]
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
49 if "select_max_features" in options:
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
50 if options["select_max_features"]["max_features"] == "number_input":
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
51 options["select_max_features"]["max_features"] = options["select_max_features"]["num_max_features"]
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
52 options["select_max_features"].pop("num_max_features")
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
53 options["max_features"] = options["select_max_features"]["max_features"]
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
54 options.pop("select_max_features")
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
55 if "presort" in options:
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
56 if options["presort"] == "true":
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
57 options["presort"] = True
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
58 if options["presort"] == "false":
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
59 options["presort"] = False
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
60 if "min_samples_leaf" in options and options["min_samples_leaf"] == 1.0:
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
61 options["min_samples_leaf"] = 1
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
62 if "min_samples_split" in options and options["min_samples_split"] > 1.0:
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
63 options["min_samples_split"] = int(options["min_samples_split"])
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
64
18
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
65 X, y = get_X_y(params, infile1, infile2)
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
66
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
67 my_class = getattr(sklearn.ensemble, algorithm)
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
68 estimator = my_class(**options)
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
69 estimator.fit(X,y)
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
70 pickle.dump(estimator,open(outfile_fit, 'w+'), pickle.HIGHEST_PROTOCOL)
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
71
18
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
72 else:
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
73 classifier_object = pickle.load(open(infile_model, 'r'))
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
74 header = 'infer' if params["selected_tasks"]["header"] else None
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
75 data = pandas.read_csv(infile_data, sep='\t', header=header, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False)
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
76 prediction = classifier_object.predict(data)
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
77 prediction_df = pandas.DataFrame(prediction, columns=["predicted"])
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
78 res = pandas.concat([data, prediction_df], axis=1)
0070e491573f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 7c2fd140e89605fe689c39e21d70a400545e38cf
bgruening
parents: 17
diff changeset
79 res.to_csv(path_or_buf = outfile_predict, sep="\t", index=False)
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
80
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
81 ]]>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
82 </configfile>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
83 </configfiles>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
84 <inputs>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
85 <expand macro="sl_Conditional" model="zip">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
86 <param name="selected_algorithm" type="select" label="Select an ensemble method:">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
87 <option value="RandomForestClassifier" selected="true">Random forest classifier</option>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
88 <option value="AdaBoostClassifier">Ada boost classifier</option>
9
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
89 <option value="GradientBoostingClassifier">Gradient Boosting Classifier</option>
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
90 <option value="RandomForestRegressor">Random forest regressor</option>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
91 <option value="AdaBoostRegressor">Ada boost regressor</option>
9
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
92 <option value="GradientBoostingRegressor">Gradient Boosting Regressor</option>
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
93 </param>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
94 <when value="RandomForestClassifier">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
95 <expand macro="sl_mixed_input"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
96 <section name="options" title="Advanced Options" expanded="False">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
97 <expand macro="n_estimators"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
98 <expand macro="criterion"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
99 <expand macro="max_features"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
100 <expand macro="max_depth"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
101 <expand macro="min_samples_split"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
102 <expand macro="min_samples_leaf"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
103 <expand macro="min_weight_fraction_leaf"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
104 <expand macro="max_leaf_nodes"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
105 <expand macro="bootstrap"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
106 <expand macro="warm_start" checked="false"/>
9
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
107 <expand macro="n_jobs"/>
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
108 <expand macro="random_state"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
109 <expand macro="oob_score"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
110 <!--class_weight=None-->
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
111 </section>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
112 </when>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
113 <when value="AdaBoostClassifier">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
114 <expand macro="sl_mixed_input"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
115 <section name="options" title="Advanced Options" expanded="False">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
116 <!--base_estimator=None-->
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
117 <expand macro="n_estimators" default_value="50"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
118 <expand macro="learning_rate"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
119 <param argument="algorithm" type="select" label="Boosting algorithm" help=" ">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
120 <option value="SAMME.R" selected="true">SAMME.R</option>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
121 <option value="SAMME">SAMME</option>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
122 </param>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
123 <expand macro="random_state"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
124 </section>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
125 </when>
9
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
126 <when value="GradientBoostingClassifier">
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
127 <expand macro="sl_mixed_input"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
128 <section name="options" title="Advanced Options" expanded="False">
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
129 <!--base_estimator=None-->
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
130 <param argument="loss" type="select" label="Loss function">
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
131 <option value="deviance" selected="true">deviance - logistic regression with probabilistic outputs</option>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
132 <option value="exponential">exponential - gradient boosting recovers the AdaBoost algorithm</option>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
133 </param>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
134 <expand macro="learning_rate" default_value='0.1'/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
135 <expand macro="n_estimators" default_value="100" help="The number of boosting stages to perform"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
136 <expand macro="max_depth" default_value="3" help="maximum depth of the individual regression estimators"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
137 <expand macro="criterion2">
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
138 <option value="friedman_mse" selected="true">friedman_mse - mean squared error with improvement score by Friedman</option>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
139 </expand>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
140 <expand macro="min_samples_split" type="float"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
141 <expand macro="min_samples_leaf" type="float" label="The minimum number of samples required to be at a leaf node"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
142 <expand macro="min_weight_fraction_leaf"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
143 <expand macro="subsample"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
144 <expand macro="max_features"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
145 <expand macro="max_leaf_nodes"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
146 <expand macro="min_impurity_decrease"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
147 <expand macro="verbose"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
148 <expand macro="warm_start" checked="false"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
149 <expand macro="random_state"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
150 <expand macro="presort"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
151 </section>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
152 </when>
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
153 <when value="RandomForestRegressor">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
154 <expand macro="sl_mixed_input"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
155 <section name="options" title="Advanced Options" expanded="False">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
156 <expand macro="n_estimators"/>
9
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
157 <expand macro="criterion2"/>
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
158 <expand macro="max_features"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
159 <expand macro="max_depth"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
160 <expand macro="min_samples_split"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
161 <expand macro="min_samples_leaf"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
162 <expand macro="min_weight_fraction_leaf"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
163 <expand macro="max_leaf_nodes"/>
9
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
164 <expand macro="min_impurity_decrease"/>
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
165 <expand macro="bootstrap"/>
9
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
166 <expand macro="oob_score"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
167 <expand macro="n_jobs"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
168 <expand macro="random_state"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
169 <expand macro="verbose"/>
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
170 <expand macro="warm_start" checked="false"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
171 </section>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
172 </when>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
173 <when value="AdaBoostRegressor">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
174 <expand macro="sl_mixed_input"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
175 <section name="options" title="Advanced Options" expanded="False">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
176 <!--base_estimator=None-->
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
177 <expand macro="n_estimators" default_value="50"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
178 <expand macro="learning_rate"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
179 <param argument="loss" type="select" label="Loss function" optional="true" help="Used when updating the weights after each boosting iteration. ">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
180 <option value="linear" selected="true">linear</option>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
181 <option value="square">square</option>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
182 <option value="exponential">exponential</option>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
183 </param>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
184 <expand macro="random_state"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
185 </section>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
186 </when>
9
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
187 <when value="GradientBoostingRegressor">
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
188 <expand macro="sl_mixed_input"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
189 <section name="options" title="Advanced Options" expanded="False">
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
190 <param argument="loss" type="select" label="Loss function">
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
191 <option value="ls" selected="true">ls - least squares regression</option>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
192 <option value="lad">lad - least absolute deviation</option>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
193 <option value="huber">huber - combination of least squares regression and least absolute deviation</option>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
194 <option value="quantile">quantile - use alpha to specify the quantile</option>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
195 </param>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
196 <expand macro="learning_rate" default_value="0.1"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
197 <expand macro="n_estimators" default_value="100" help="The number of boosting stages to perform"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
198 <expand macro="max_depth" default_value="3" help="maximum depth of the individual regression estimators"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
199 <expand macro="criterion2">
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
200 <option value="friedman_mse" selected="true">friedman_mse - mean squared error with improvement score by Friedman</option>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
201 </expand>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
202 <expand macro="min_samples_split" type="float"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
203 <expand macro="min_samples_leaf" type="float" label="The minimum number of samples required to be at a leaf node"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
204 <expand macro="min_weight_fraction_leaf"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
205 <expand macro="subsample"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
206 <expand macro="max_features"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
207 <expand macro="max_leaf_nodes"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
208 <expand macro="min_impurity_decrease"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
209 <param argument="alpha" type="float" value="0.9" label="alpha" help="The alpha-quantile of the huber loss function and the quantile loss function" />
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
210 <!--base_estimator=None-->
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
211 <expand macro="verbose"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
212 <expand macro="warm_start" checked="false"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
213 <expand macro="random_state"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
214 <expand macro="presort"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
215 </section>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
216 </when>
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
217 </expand>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
218 </inputs>
4
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
219
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
220 <expand macro="output"/>
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
221
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
222 <tests>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
223 <test>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
224 <param name="infile1" value="train.tabular" ftype="tabular"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
225 <param name="infile2" value="train.tabular" ftype="tabular"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
226 <param name="col1" value="1,2,3,4"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
227 <param name="col2" value="5"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
228 <param name="selected_task" value="train"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
229 <param name="selected_algorithm" value="RandomForestClassifier"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
230 <param name="random_state" value="10"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
231 <output name="outfile_fit" file="rfc_model01" compare="sim_size" delta="500"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
232 </test>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
233 <test>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
234 <param name="infile_model" value="rfc_model01" ftype="zip"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
235 <param name="infile_data" value="test.tabular" ftype="tabular"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
236 <param name="selected_task" value="load"/>
4
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
237 <output name="outfile_predict" file="rfc_result01" compare="sim_size" delta="500"/>
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
238 </test>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
239 <test>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
240 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
241 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
242 <param name="col1" value="1,2,3,4,5"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
243 <param name="col2" value="6"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
244 <param name="selected_task" value="train"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
245 <param name="selected_algorithm" value="RandomForestRegressor"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
246 <param name="random_state" value="10"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
247 <output name="outfile_fit" file="rfr_model01" compare="sim_size" delta="500"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
248 </test>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
249 <test>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
250 <param name="infile_model" value="rfr_model01" ftype="zip"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
251 <param name="infile_data" value="regression_test.tabular" ftype="tabular"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
252 <param name="selected_task" value="load"/>
4
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
253 <output name="outfile_predict" file="rfr_result01" compare="sim_size" delta="500"/>
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
254 </test>
9
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
255 <test>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
256 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
257 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
258 <param name="header1" value="True"/>
14
923ecece9e9c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 97c4f22cdcfa6cddeeffc7b102c418a7ff12a888
bgruening
parents: 9
diff changeset
259 <param name="selected_column_selector_option" value="all_columns"/>
9
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
260 <param name="header2" value="True"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
261 <param name="col2" value="1"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
262 <param name="selected_task" value="train"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
263 <param name="selected_algorithm" value="GradientBoostingRegressor"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
264 <param name="max_features" value="number_input"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
265 <param name="num_max_features" value=""/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
266 <param name="random_state" value="42"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
267 <output name="outfile_fit" file="gbr_model01" compare="sim_size" delta="500"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
268 </test>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
269 <test>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
270 <param name="infile_model" value="gbr_model01" ftype="zip"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
271 <param name="infile_data" value="regression_test_X.tabular" ftype="tabular"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
272 <param name="selected_task" value="load"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
273 <param name="header" value="True"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
274 <output name="outfile_predict" file="gbr_prediction_result01.tabular" compare="sim_size" delta="500"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
275 </test>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
276 <test>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
277 <param name="infile1" value="train.tabular" ftype="tabular"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
278 <param name="infile2" value="train.tabular" ftype="tabular"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
279 <param name="col1" value="1,2,3,4"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
280 <param name="col2" value="5"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
281 <param name="selected_task" value="train"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
282 <param name="selected_algorithm" value="GradientBoostingClassifier"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
283 <output name="outfile_fit" file="gbc_model01" compare="sim_size" delta="500"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
284 </test>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
285 <test>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
286 <param name="infile_model" value="gbc_model01" ftype="zip"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
287 <param name="infile_data" value="test.tabular" ftype="tabular"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
288 <param name="selected_task" value="load"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
289 <output name="outfile_predict" file="gbc_result01" compare="sim_size" delta="500"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02
bgruening
parents: 8
diff changeset
290 </test>
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
291 </tests>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
292 <help><![CDATA[
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
293 ***What it does***
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
294 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`_.
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
295
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
296 .. _`Scikit-learn ensemble`: http://scikit-learn.org/stable/modules/ensemble.html
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
297
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
298 **1 - Methods**
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
299 There are two groups of operations available:
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
300
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
301 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.
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
302
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
303 2 - Load a model and predict : An existing model predicts the class labels (or regression values) for a new dataset.
4
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
304
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
305 **2 - Trainig input**
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
306 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:
4
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
307
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
308 **Sample tabular features dataset**
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
309 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:
4
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
310
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
311 ::
4
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
312
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
313 4.01163365529 -6.10797684314 8.29829894763 1
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
314 10.0788438916 1.59539821454 10.0684278289 0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
315 -5.17607775503 -0.878286135332 6.92941850665 2
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
316 4.00975406235 -7.11847496542 9.3802423585 1
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
317 4.61204065139 -5.71217537352 9.12509610964 1
4
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
318
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
319
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
320 **Sample sparse features dataset**
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
321 In this case you cannot specifiy a column range.
4
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
322
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
323 ::
4
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
324
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
325 4 1048577 8738
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
326 1 271 0.02083333333333341
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
327 1 1038 0.02461995616119806
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
328 2 829017 0.01629088031127686
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
329 2 829437 0.01209127083516686
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
330 2 830752 0.02535100632816968
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
331 3 1047487 0.01485722929945572
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
332 3 1047980 0.02640566620767753
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
333 3 1048475 0.01665869913262564
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
334 4 608 0.01662975263094352
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
335 4 1651 0.02519674277562741
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
336 4 4053 0.04223659971350601
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
337
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
338
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
339 **2 - Trainig output**
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
340 The trained model is generated and output in the form of a binary file.
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
341
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
342
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
343 **3 - Prediction input**
4
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
344
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
345 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.
4
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
346
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
347
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
348 .. class:: warningmark
4
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
349
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
350 The number of feature columns must be the same in training and prediction datasets!
4
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
351
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
352
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
353 **3 - Prediction output**
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
354 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.
4
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents: 2
diff changeset
355
0
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
356 ]]></help>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
357 <expand macro="sklearn_citation"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417
bgruening
parents:
diff changeset
358 </tool>