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annotate feature_selection.xml @ 5:de0950f27aba draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 64158f357e708f0b60d2669d92d614f7aee34c0e
author bgruening
date Wed, 06 Jun 2018 17:38:50 -0400
parents 73c12f296b1c
children dc574d9778bd
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1 <tool id="sklearn_feature_selection" name="Feature Selection" version="@VERSION@.1">
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2 <description>module, including univariate filter selection methods and recursive feature elimination algorithm</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 </macros>
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6 <expand macro="python_requirements"/>
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7 <expand macro="macro_stdio"/>
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8 <version_command>echo "@VERSION@"</version_command>
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9 <command>
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10 <![CDATA[
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11 python "$feature_selection_script" '$inputs'
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12 ]]>
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13 </command>
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14 <configfiles>
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15 <inputs name="inputs" />
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16 <configfile name="feature_selection_script">
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17 <![CDATA[
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18 import sys
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19 import json
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20 import pandas
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21 import pickle
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22 import numpy as np
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23 import sklearn.feature_selection
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24 from sklearn import svm, linear_model, ensemble
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26 @COLUMNS_FUNCTION@
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27
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28 @FEATURE_SELECTOR_FUNCTION@
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29
0
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30 input_json_path = sys.argv[1]
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31 params = json.load(open(input_json_path, "r"))
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32
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33 ## Read features
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34 features_has_header = params["input_options"]["header1"]
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35 input_type = params["input_options"]["selected_input"]
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36 if input_type=="tabular":
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37 header = 'infer' if features_has_header else None
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38 column_option = params["input_options"]["column_selector_options_1"]["selected_column_selector_option"]
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39 if column_option in ["by_index_number", "all_but_by_index_number"]:
4
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40 c = params["input_options"]["column_selector_options_1"]["col1"]
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41 else:
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42 c = None
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43 X, input_df = read_columns(
0
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44 "$input_options.infile1",
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45 c = c,
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46 c_option = column_option,
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47 return_df = True,
0
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48 sep='\t',
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49 header=header,
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50 parse_dates=True
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51 )
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52 else:
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53 X = mmread(open("$input_options.infile1", 'r'))
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54
2
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55 ## Read labels
0
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56 header = 'infer' if params["input_options"]["header2"] else None
4
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57 column_option = params["input_options"]["column_selector_options_2"]["selected_column_selector_option2"]
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58 if column_option in ["by_index_number", "all_but_by_index_number"]:
4
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59 c = params["input_options"]["column_selector_options_2"]["col2"]
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60 else:
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61 c = None
0
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62 y = read_columns(
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63 "$input_options.infile2",
4
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64 c = c,
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65 c_option = column_option,
0
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66 sep='\t',
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67 header=header,
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68 parse_dates=True
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69 )
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70 y=y.ravel()
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71
2
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72 ## Create feature selector
3
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73 new_selector = feature_selector(params['feature_selection_algorithms'])
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74 if params['feature_selection_algorithms']['selected_algorithm'] != 'SelectFromModel' or \
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75 'extra_estimator' not in params['feature_selection_algorithms'] or \
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76 params['feature_selection_algorithms']['extra_estimator']['has_estimator'] != 'no_load' :
2
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77 new_selector.fit(X, y)
0
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78
2
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79 ## Transform to select features
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80 selected_names = None
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81 if "$select_methods.selected_method" == "fit_transform":
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82 res = new_selector.transform(X)
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83 if features_has_header:
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84 selected_names = input_df.columns[new_selector.get_support(indices=True)]
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85 else:
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86 res = new_selector.get_support(params["select_methods"]["indices"])
0
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87
2
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88 res = pandas.DataFrame(res, columns = selected_names)
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89 res.to_csv(path_or_buf="$outfile", sep='\t', index=False)
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90
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91
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92 ]]>
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93 </configfile>
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94 </configfiles>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
95 <inputs>
2
5a06c81f044d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 0
diff changeset
96 <expand macro="feature_selection_all" />
0
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
97 <expand macro="feature_selection_methods" />
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
98 <expand macro="sl_mixed_input"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
99 </inputs>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
100 <outputs>
2
5a06c81f044d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
bgruening
parents: 0
diff changeset
101 <data format="tabular" name="outfile"/>
0
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
102 </outputs>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
103 <tests>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
104 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
105 <param name="selected_algorithm" value="SelectFromModel"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
106 <param name="has_estimator" value="no"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
107 <param name="new_estimator" value="ensemble.RandomForestRegressor(n_estimators = 1000, random_state = 42)"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
108 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
109 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
110 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
111 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
112 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
113 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
114 <output name="outfile" file="feature_selection_result01"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
115 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
116 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
117 <param name="selected_algorithm" value="GenericUnivariateSelect"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
118 <param name="param" value="20"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
119 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
120 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
121 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
122 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
123 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
124 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
125 <output name="outfile" file="feature_selection_result02"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
126 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
127 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
128 <param name="selected_algorithm" value="SelectPercentile"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
129 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
130 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
131 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
132 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
133 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
134 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
135 <output name="outfile" file="feature_selection_result03"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
136 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
137 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
138 <param name="selected_algorithm" value="SelectKBest"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
139 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
140 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
141 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
142 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
143 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
144 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
145 <output name="outfile" file="feature_selection_result04"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
146 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
147 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
148 <param name="selected_algorithm" value="SelectFpr"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
149 <param name="alpha" value="0.05"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
150 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
151 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
152 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
153 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
154 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
155 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
156 <output name="outfile" file="feature_selection_result05"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
157 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
158 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
159 <param name="selected_algorithm" value="SelectFdr"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
160 <param name="alpha" value="0.05"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
161 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
162 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
163 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
164 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
165 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
166 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
167 <output name="outfile" file="feature_selection_result06"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
168 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
169 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
170 <param name="selected_algorithm" value="SelectFwe"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
171 <param name="alpha" value="0.05"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
172 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
173 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
174 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
175 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
176 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
177 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
178 <output name="outfile" file="feature_selection_result07"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
179 </test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
180 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
181 <param name="selected_algorithm" value="RFE"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
182 <param name="has_estimator" value="no"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
183 <param name="new_estimator" value="ensemble.RandomForestRegressor(n_estimators = 1000, random_state = 42)"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
184 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
185 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
186 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
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187 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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188 <param name="col2" value="1"/>
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189 <param name="header2" value="True"/>
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190 <output name="outfile" file="feature_selection_result08"/>
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191 </test>
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192 <test>
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193 <param name="selected_algorithm" value="RFECV"/>
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194 <param name="has_estimator" value="no"/>
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195 <param name="new_estimator" value="ensemble.RandomForestRegressor(n_estimators = 1000, random_state = 42)"/>
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196 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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197 <param name="header1" value="True"/>
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198 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
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199 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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200 <param name="col2" value="1"/>
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201 <param name="header2" value="True"/>
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202 <output name="outfile" file="feature_selection_result09"/>
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203 </test>
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204 <test>
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205 <param name="selected_algorithm" value="VarianceThreshold"/>
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206 <param name="threshold" value="0.1"/>
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207 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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208 <param name="header1" value="True"/>
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209 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
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210 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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211 <param name="col2" value="1"/>
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212 <param name="header2" value="True"/>
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213 <output name="outfile" file="feature_selection_result10"/>
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214 </test>
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215 </tests>
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216 <help>
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217 <![CDATA[
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218 **What it does**
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219 This tool provides several loss, score, and utility functions to measure classification performance. Some metrics might require probability estimates of the positive class, confidence values, or binary decisions values. This tool is based on
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220 sklearn.metrics package.
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221 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
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222
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223 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
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224 ]]>
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225 </help>
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226 <expand macro="sklearn_citation"/>
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227 </tool>