sklearn_ensemble: ensemble.xml annotate

annotate ensemble.xml @ 9:e4fcbbc81083 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02

author	bgruening
date	Tue, 10 Apr 2018 15:15:18 -0400
parents	ea8b1c89c20b
children	923ecece9e9c

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@
ea8b1c89c20b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit cea052cf3b8dd4f3620253bd222e126de32e7466 bgruening parents: 6 diff changeset	26
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	27 input_json_path = sys.argv[1]
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	28 params = json.load(open(input_json_path, "r"))
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	29
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	30 #if $selected_tasks.selected_task == "train":
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	31
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	32 algorithm = params["selected_tasks"]["selected_algorithms"]["selected_algorithm"]
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	33 options = params["selected_tasks"]["selected_algorithms"]["options"]
9 e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	34 if "select_max_features" in options:
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	35 if options["select_max_features"]["max_features"] == "number_input":
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	36 options["select_max_features"]["max_features"] = options["select_max_features"]["num_max_features"]
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	37 options["select_max_features"].pop("num_max_features")
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	38 options["max_features"] = options["select_max_features"]["max_features"]
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	39 options.pop("select_max_features")
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	40 if "presort" in options:
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	41 if options["presort"] == "true":
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	42 options["presort"] = True
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	43 if options["presort"] == "false":
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	44 options["presort"] = False
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	45 if "min_samples_leaf" in options and options["min_samples_leaf"] == 1.0:
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	46 options["min_samples_leaf"] = 1
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	47 if "min_samples_split" in options and options["min_samples_split"] > 1.0:
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	48 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	49 input_type = params["selected_tasks"]["selected_algorithms"]["input_options"]["selected_input"]
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	50 if input_type=="tabular":
8 ea8b1c89c20b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit cea052cf3b8dd4f3620253bd222e126de32e7466 bgruening parents: 6 diff changeset	51 header = 'infer' if params["selected_tasks"]["selected_algorithms"]["input_options"]["header1"] else None
6 4c2fae2db5d1 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76 bgruening parents: 4 diff changeset	52 X = read_columns(
4c2fae2db5d1 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76 bgruening parents: 4 diff changeset	53 "$selected_tasks.selected_algorithms.input_options.infile1",
4c2fae2db5d1 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76 bgruening parents: 4 diff changeset	54 "$selected_tasks.selected_algorithms.input_options.col1",
4c2fae2db5d1 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76 bgruening parents: 4 diff changeset	55 sep='\t',
8 ea8b1c89c20b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit cea052cf3b8dd4f3620253bd222e126de32e7466 bgruening parents: 6 diff changeset	56 header=header,
6 4c2fae2db5d1 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76 bgruening parents: 4 diff changeset	57 parse_dates=True
4c2fae2db5d1 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76 bgruening parents: 4 diff changeset	58 )
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	59 else:
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	60 X = mmread(open("$selected_tasks.selected_algorithms.input_options.infile1", 'r'))
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	61
8 ea8b1c89c20b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit cea052cf3b8dd4f3620253bd222e126de32e7466 bgruening parents: 6 diff changeset	62 header = 'infer' if params["selected_tasks"]["selected_algorithms"]["input_options"]["header2"] else None
6 4c2fae2db5d1 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76 bgruening parents: 4 diff changeset	63 y = read_columns(
4c2fae2db5d1 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76 bgruening parents: 4 diff changeset	64 "$selected_tasks.selected_algorithms.input_options.infile2",
4c2fae2db5d1 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76 bgruening parents: 4 diff changeset	65 "$selected_tasks.selected_algorithms.input_options.col2",
4c2fae2db5d1 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76 bgruening parents: 4 diff changeset	66 sep='\t',
8 ea8b1c89c20b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit cea052cf3b8dd4f3620253bd222e126de32e7466 bgruening parents: 6 diff changeset	67 header=header,
6 4c2fae2db5d1 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76 bgruening parents: 4 diff changeset	68 parse_dates=True
4c2fae2db5d1 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76 bgruening parents: 4 diff changeset	69 )
9 e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	70 y=y.ravel()
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	71
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	72 my_class = getattr(sklearn.ensemble, algorithm)
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	73 estimator = my_class(**options)
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	74 estimator.fit(X,y)
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	75 pickle.dump(estimator,open("$outfile_fit", 'w+'), pickle.HIGHEST_PROTOCOL)
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	76
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	77 #else:
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	78 classifier_object = pickle.load(open("$selected_tasks.infile_model", 'r'))
9 e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	79 header = 'infer' if params["selected_tasks"]["header"] else None
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	80 data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=header, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False)
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	81 prediction = classifier_object.predict(data)
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	82 prediction_df = pandas.DataFrame(prediction)
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	83 res = pandas.concat([data, prediction_df], axis=1)
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	84 res.to_csv(path_or_buf = "$outfile_predict", sep="\t", index=False)
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	85 #end if
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	86
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	87 ]]>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	88 </configfile>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	89 </configfiles>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	90 <inputs>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	91 <expand macro="sl_Conditional" model="zip">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	92 <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	93 <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	94 <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	95 <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	96 <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	97 <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	98 <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	99 </param>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	100 <when value="RandomForestClassifier">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	101 <expand macro="sl_mixed_input"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	102 <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	103 <expand macro="n_estimators"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	104 <expand macro="criterion"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	105 <expand macro="max_features"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	106 <expand macro="max_depth"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	107 <expand macro="min_samples_split"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	108 <expand macro="min_samples_leaf"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	109 <expand macro="min_weight_fraction_leaf"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	110 <expand macro="max_leaf_nodes"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	111 <expand macro="bootstrap"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	112 <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	113 <expand macro="n_jobs"/>
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	114 <expand macro="random_state"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	115 <expand macro="oob_score"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	116 <!--class_weight=None-->
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	117 </section>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	118 </when>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	119 <when value="AdaBoostClassifier">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	120 <expand macro="sl_mixed_input"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	121 <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	122 <!--base_estimator=None-->
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	123 <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	124 <expand macro="learning_rate"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	125 <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	126 <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	127 <option value="SAMME">SAMME</option>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	128 </param>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	129 <expand macro="random_state"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	130 </section>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	131 </when>
9 e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	132 <when value="GradientBoostingClassifier">
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	133 <expand macro="sl_mixed_input"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	134 <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	135 <!--base_estimator=None-->
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	136 <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	137 <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	138 <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	139 </param>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	140 <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	141 <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	142 <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	143 <expand macro="criterion2">
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	144 <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	145 </expand>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	146 <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	147 <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	148 <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	149 <expand macro="subsample"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	150 <expand macro="max_features"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	151 <expand macro="max_leaf_nodes"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	152 <expand macro="min_impurity_decrease"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	153 <expand macro="verbose"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	154 <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	155 <expand macro="random_state"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	156 <expand macro="presort"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	157 </section>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	158 </when>
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	159 <when value="RandomForestRegressor">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	160 <expand macro="sl_mixed_input"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	161 <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	162 <expand macro="n_estimators"/>
9 e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	163 <expand macro="criterion2"/>
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	164 <expand macro="max_features"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	165 <expand macro="max_depth"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	166 <expand macro="min_samples_split"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	167 <expand macro="min_samples_leaf"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	168 <expand macro="min_weight_fraction_leaf"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	169 <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	170 <expand macro="min_impurity_decrease"/>
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	171 <expand macro="bootstrap"/>
9 e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	172 <expand macro="oob_score"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	173 <expand macro="n_jobs"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	174 <expand macro="random_state"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	175 <expand macro="verbose"/>
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	176 <expand macro="warm_start" checked="false"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	177 </section>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	178 </when>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	179 <when value="AdaBoostRegressor">
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	180 <expand macro="sl_mixed_input"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	181 <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	182 <!--base_estimator=None-->
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	183 <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	184 <expand macro="learning_rate"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	185 <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	186 <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	187 <option value="square">square</option>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	188 <option value="exponential">exponential</option>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	189 </param>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	190 <expand macro="random_state"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	191 </section>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	192 </when>
9 e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	193 <when value="GradientBoostingRegressor">
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	194 <expand macro="sl_mixed_input"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	195 <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	196 <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	197 <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	198 <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	199 <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	200 <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	201 </param>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	202 <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	203 <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	204 <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	205 <expand macro="criterion2">
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	206 <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	207 </expand>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	208 <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	209 <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	210 <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	211 <expand macro="subsample"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	212 <expand macro="max_features"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	213 <expand macro="max_leaf_nodes"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	214 <expand macro="min_impurity_decrease"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	215 <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	216 <!--base_estimator=None-->
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	217 <expand macro="verbose"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	218 <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	219 <expand macro="random_state"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	220 <expand macro="presort"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	221 </section>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	222 </when>
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	223 </expand>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	224 </inputs>
4 3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: 2 diff changeset	225
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: 2 diff changeset	226 <expand macro="output"/>
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: 2 diff changeset	227
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	228 <tests>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	229 <test>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	230 <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	231 <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	232 <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	233 <param name="col2" value="5"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	234 <param name="selected_task" value="train"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	235 <param name="selected_algorithm" value="RandomForestClassifier"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	236 <param name="random_state" value="10"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	237 <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	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="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	241 <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	242 <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	243 <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	244 </test>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	245 <test>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	246 <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	247 <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	248 <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	249 <param name="col2" value="6"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	250 <param name="selected_task" value="train"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	251 <param name="selected_algorithm" value="RandomForestRegressor"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	252 <param name="random_state" value="10"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	253 <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	254 </test>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	255 <test>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	256 <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	257 <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	258 <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	259 <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	260 </test>
9 e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	261 <test>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	262 <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	263 <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	264 <param name="header1" value="True"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	265 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	266 <param name="header2" value="True"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	267 <param name="col2" value="1"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	268 <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	269 <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	270 <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	271 <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	272 <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	273 <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	274 </test>
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 <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	277 <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	278 <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	279 <param name="header" value="True"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	280 <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	281 </test>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	282 <test>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	283 <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	284 <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	285 <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	286 <param name="col2" value="5"/>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	287 <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	288 <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	289 <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	290 </test>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	291 <test>
e4fcbbc81083 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 35fa73d6e9ba8f0789ddfb743d893d950a68af02 bgruening parents: 8 diff changeset	292 <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	293 <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	294 <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	295 <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	296 </test>
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	297 </tests>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	298 <help><![CDATA[
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	299 *What it does*
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	300 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	301
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	302 .. _`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	303
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	304 1 - Methods
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	305 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	306
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	307 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	308
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	309 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	310
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	311 2 - Trainig input
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	312 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	313
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	314 Sample tabular features dataset
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	315 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	316
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	317 ::
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 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	320 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	321 -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	322 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	323 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	324
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	325
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	326 Sample sparse features dataset
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	327 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	328
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	329 ::
4 3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: 2 diff changeset	330
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	331 4 1048577 8738
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	332 1 271 0.02083333333333341
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	333 1 1038 0.02461995616119806
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	334 2 829017 0.01629088031127686
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	335 2 829437 0.01209127083516686
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	336 2 830752 0.02535100632816968
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	337 3 1047487 0.01485722929945572
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	338 3 1047980 0.02640566620767753
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	339 3 1048475 0.01665869913262564
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	340 4 608 0.01662975263094352
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	341 4 1651 0.02519674277562741
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	342 4 4053 0.04223659971350601
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	343
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	344
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	345 2 - Trainig output
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	346 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	347
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	348
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	349 3 - Prediction input
4 3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: 2 diff changeset	350
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	351 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	352
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	353
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	354 .. class:: warningmark
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 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	357
3bc536788043 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: 2 diff changeset	358
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	359 3 - Prediction output
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	360 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	361
0 31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	362 ]]></help>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	363 <expand macro="sklearn_citation"/>
31fd07e0acdb planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 6c002ea2995c85f5f16adb2ef1c6be82dfbc5417 bgruening parents: diff changeset	364 </tool>

Mercurial > repos > bgruening > sklearn_ensemble

annotate ensemble.xml @ 9:e4fcbbc81083 draft