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annotate feature_selection.xml @ 14:dc411a215138 draft

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author bgruening
date Thu, 23 Aug 2018 16:16:26 -0400
parents f8dfdb47508b
children 026667802750
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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 os
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20 import json
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21 import pandas
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22 import sklearn.feature_selection
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24 execfile("$__tool_directory__/sk_whitelist.py")
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25 execfile("$__tool_directory__/utils.py", globals())
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27 safe_eval = SafeEval()
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28
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29 input_json_path = sys.argv[1]
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30 with open(input_json_path, "r") as param_handler:
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31 params = json.load(param_handler)
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32
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33 #handle cheetah
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34 #if $fs_algorithm_selector.selected_algorithm == "SelectFromModel"\
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35 and $fs_algorithm_selector.model_inputter.input_mode == "prefitted":
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36 params['fs_algorithm_selector']['model_inputter']['fitted_estimator'] =\
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37 "$fs_algorithm_selector.model_inputter.fitted_estimator"
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38 #end if
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39
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40 # Read features
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41 features_has_header = params["input_options"]["header1"]
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42 input_type = params["input_options"]["selected_input"]
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43 if input_type=="tabular":
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44 header = 'infer' if features_has_header else None
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45 column_option = params["input_options"]["column_selector_options_1"]["selected_column_selector_option"]
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46 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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47 c = params["input_options"]["column_selector_options_1"]["col1"]
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48 else:
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49 c = None
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50 X, input_df = read_columns(
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51 "$input_options.infile1",
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52 c = c,
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53 c_option = column_option,
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54 return_df = True,
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55 sep='\t',
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56 header=header,
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57 parse_dates=True
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58 )
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59 else:
9
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60 X = mmread("$input_options.infile1")
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61
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62 # Read labels
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63 header = 'infer' if params["input_options"]["header2"] else None
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64 column_option = params["input_options"]["column_selector_options_2"]["selected_column_selector_option2"]
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65 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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66 c = params["input_options"]["column_selector_options_2"]["col2"]
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67 else:
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68 c = None
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69 y = read_columns(
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70 "$input_options.infile2",
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71 c = c,
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72 c_option = column_option,
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73 sep='\t',
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74 header=header,
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75 parse_dates=True
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76 )
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77 y=y.ravel()
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78
10
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79 # Create feature selector
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80 new_selector = feature_selector(params['fs_algorithm_selector'])
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81 if params['fs_algorithm_selector']['selected_algorithm'] != 'SelectFromModel'\
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82 or params['fs_algorithm_selector']['model_inputter']['input_mode'] != 'prefitted' :
2
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83 new_selector.fit(X, y)
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84
2
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85 ## Transform to select features
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86 selected_names = None
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87 if "$output_method_selector.selected_method" == "fit_transform":
2
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88 res = new_selector.transform(X)
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89 if features_has_header:
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90 selected_names = input_df.columns[new_selector.get_support(indices=True)]
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91 else:
10
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92 res = new_selector.get_support(params["output_method_selector"]["indices"])
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diff changeset
93
2
2eb90e73f0d5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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diff changeset
94 res = pandas.DataFrame(res, columns = selected_names)
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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95 res.to_csv(path_or_buf="$outfile", sep='\t', index=False)
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96
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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97
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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98 ]]>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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99 </configfile>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
100 </configfiles>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
101 <inputs>
10
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102 <expand macro="feature_selection_all">
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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103 <expand macro="fs_selectfrommodel_prefitted"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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104 </expand>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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105 <expand macro="feature_selection_output_mothods" />
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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106 <expand macro="sl_mixed_input"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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107 </inputs>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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108 <outputs>
2
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109 <data format="tabular" name="outfile"/>
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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110 </outputs>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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111 <tests>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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112 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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113 <param name="selected_algorithm" value="SelectFromModel"/>
10
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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114 <param name="input_mode" value="new"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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115 <param name="selected_module" value="ensemble"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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116 <param name="selected_estimator" value="RandomForestRegressor"/>
13
f8dfdb47508b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
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117 <param name="text_params" value="n_estimators=10, random_state=10"/>
10
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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118 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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119 <param name="header1" value="false"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
120 <param name="col1" value="1,2,3,4,5"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
121 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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122 <param name="col2" value="6"/>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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123 <param name="header2" value="false"/>
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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124 <output name="outfile" file="feature_selection_result01"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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125 </test>
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126 <test>
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127 <param name="selected_algorithm" value="GenericUnivariateSelect"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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128 <param name="param" value="20"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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129 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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130 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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131 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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132 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
133 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
134 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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135 <output name="outfile" file="feature_selection_result02"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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136 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
137 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
138 <param name="selected_algorithm" value="SelectPercentile"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
139 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
140 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
141 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
142 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
143 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
144 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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145 <output name="outfile" file="feature_selection_result03"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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146 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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147 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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148 <param name="selected_algorithm" value="SelectKBest"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
149 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
150 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
151 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
152 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
153 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
154 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
155 <output name="outfile" file="feature_selection_result04"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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156 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
157 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
158 <param name="selected_algorithm" value="SelectFpr"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
159 <param name="alpha" value="0.05"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
160 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
161 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
162 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
163 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
164 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents:
diff changeset
165 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents:
diff changeset
166 <output name="outfile" file="feature_selection_result05"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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167 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
168 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
169 <param name="selected_algorithm" value="SelectFdr"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
170 <param name="alpha" value="0.05"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
171 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
172 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
173 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
174 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
175 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
176 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
177 <output name="outfile" file="feature_selection_result06"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
178 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
179 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
180 <param name="selected_algorithm" value="SelectFwe"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
181 <param name="alpha" value="0.05"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
182 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
183 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
184 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
185 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
186 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
187 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
188 <output name="outfile" file="feature_selection_result07"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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189 </test>
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190 <test>
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191 <param name="selected_algorithm" value="RFE"/>
10
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192 <param name="input_mode" value="new"/>
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193 <param name="selected_module" value="ensemble"/>
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194 <param name="selected_estimator" value="RandomForestRegressor"/>
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195 <param name="text_params" value="n_estimators=10, random_state=10"/>
10
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196 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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197 <param name="header1" value="false"/>
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198 <param name="col1" value="1,2,3,4,5"/>
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199 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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200 <param name="col2" value="6"/>
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201 <param name="header2" value="false"/>
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202 <output name="outfile" file="feature_selection_result08"/>
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203 </test>
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204 <test>
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205 <param name="selected_algorithm" value="RFECV"/>
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206 <param name="input_mode" value="new"/>
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207 <param name="selected_module" value="ensemble"/>
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208 <param name="selected_estimator" value="RandomForestRegressor"/>
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209 <param name="text_params" value="n_estimators=10, random_state=10"/>
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210 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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211 <param name="header1" value="false"/>
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212 <param name="col1" value="1,2,3,4,5"/>
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213 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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214 <param name="col2" value="6"/>
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215 <param name="header2" value="false"/>
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216 <output name="outfile" file="feature_selection_result09"/>
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217 </test>
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218 <test>
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219 <param name="selected_algorithm" value="VarianceThreshold"/>
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220 <param name="threshold" value="0.1"/>
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221 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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222 <param name="header1" value="True"/>
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223 <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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224 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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225 <param name="col2" value="1"/>
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226 <param name="header2" value="True"/>
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227 <output name="outfile" file="feature_selection_result10"/>
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228 </test>
6
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229 <test>
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230 <param name="selected_algorithm" value="SelectKBest"/>
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231 <param name="k" value="3"/>
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232 <param name="infile1" value="test3.tabular" ftype="tabular"/>
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233 <param name="header1" value="True"/>
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234 <param name="selected_column_selector_option" value="all_but_by_header_name"/>
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235 <param name="col1" value="target"/>
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236 <param name="infile2" value="test3.tabular" ftype="tabular"/>
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237 <param name="header2" value="True"/>
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238 <param name="selected_column_selector_option2" value="by_header_name"/>
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239 <param name="col2" value="target"/>
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240 <output name="outfile" file="feature_selection_result11"/>
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241 </test>
10
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242 <test>
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243 <param name="selected_algorithm" value="SelectFromModel"/>
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244 <param name="input_mode" value="prefitted"/>
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245 <param name="fitted_estimator" value="rfr_model01" ftype="zip"/>
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246 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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247 <param name="header1" value="false"/>
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248 <param name="col1" value="1,2,3,4,5"/>
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249 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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250 <param name="col2" value="1"/>
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251 <param name="header2" value="false"/>
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252 <output name="outfile" file="feature_selection_result12"/>
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253 </test>
0
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254 </tests>
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255 <help>
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256 <![CDATA[
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257 **What it does**
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258 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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259 sklearn.metrics package.
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260 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
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261
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262 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
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263 ]]>
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264 </help>
14
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265 <expand macro="sklearn_citation">
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266 <expand macro="skrebate_citation"/>
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267 <expand macro="xgboost_citation"/>
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268 </expand>
0
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269 </tool>