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annotate feature_selection.xml @ 13:f8dfdb47508b draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
author bgruening
date Fri, 17 Aug 2018 12:28:35 -0400
parents 96f9b73327f2
children dc411a215138
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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__/utils.py")
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26 safe_eval = SafeEval()
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27
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28 input_json_path = sys.argv[1]
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29 with open(input_json_path, "r") as param_handler:
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30 params = json.load(param_handler)
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32 #handle cheetah
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33 #if $fs_algorithm_selector.selected_algorithm == "SelectFromModel"\
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34 and $fs_algorithm_selector.model_inputter.input_mode == "prefitted":
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35 params['fs_algorithm_selector']['model_inputter']['fitted_estimator'] =\
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36 "$fs_algorithm_selector.model_inputter.fitted_estimator"
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37 #end if
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38
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39 # Read features
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40 features_has_header = params["input_options"]["header1"]
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41 input_type = params["input_options"]["selected_input"]
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42 if input_type=="tabular":
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43 header = 'infer' if features_has_header else None
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44 column_option = params["input_options"]["column_selector_options_1"]["selected_column_selector_option"]
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45 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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46 c = params["input_options"]["column_selector_options_1"]["col1"]
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47 else:
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48 c = None
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49 X, input_df = read_columns(
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50 "$input_options.infile1",
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51 c = c,
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52 c_option = column_option,
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53 return_df = True,
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54 sep='\t',
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55 header=header,
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56 parse_dates=True
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57 )
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58 else:
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59 X = mmread("$input_options.infile1")
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60
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61 # Read labels
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62 header = 'infer' if params["input_options"]["header2"] else None
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63 column_option = params["input_options"]["column_selector_options_2"]["selected_column_selector_option2"]
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64 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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65 c = params["input_options"]["column_selector_options_2"]["col2"]
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66 else:
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67 c = None
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68 y = read_columns(
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69 "$input_options.infile2",
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70 c = c,
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71 c_option = column_option,
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72 sep='\t',
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73 header=header,
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74 parse_dates=True
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75 )
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76 y=y.ravel()
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77
10
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78 # Create feature selector
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79 new_selector = feature_selector(params['fs_algorithm_selector'])
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80 if params['fs_algorithm_selector']['selected_algorithm'] != 'SelectFromModel'\
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81 or params['fs_algorithm_selector']['model_inputter']['input_mode'] != 'prefitted' :
2
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82 new_selector.fit(X, y)
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83
2
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84 ## Transform to select features
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85 selected_names = None
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86 if "$output_method_selector.selected_method" == "fit_transform":
2
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87 res = new_selector.transform(X)
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88 if features_has_header:
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89 selected_names = input_df.columns[new_selector.get_support(indices=True)]
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90 else:
10
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91 res = new_selector.get_support(params["output_method_selector"]["indices"])
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92
2
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93 res = pandas.DataFrame(res, columns = selected_names)
0
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94 res.to_csv(path_or_buf="$outfile", sep='\t', index=False)
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diff changeset
95
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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 </configfile>
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99 </configfiles>
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diff changeset
100 <inputs>
10
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101 <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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102 <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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103 </expand>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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104 <expand macro="feature_selection_output_mothods" />
0
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105 <expand macro="sl_mixed_input"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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106 </inputs>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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107 <outputs>
2
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108 <data format="tabular" name="outfile"/>
0
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109 </outputs>
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110 <tests>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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111 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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112 <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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113 <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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114 <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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115 <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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116 <param name="text_params" value="n_estimators=10, random_state=10"/>
10
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117 <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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118 <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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119 <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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120 <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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121 <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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122 <param name="header2" value="false"/>
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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123 <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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124 </test>
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125 <test>
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126 <param name="selected_algorithm" value="GenericUnivariateSelect"/>
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127 <param name="param" value="20"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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128 <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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129 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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130 <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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131 <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
132 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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133 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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134 <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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135 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
136 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
137 <param name="selected_algorithm" value="SelectPercentile"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
138 <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
139 <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
140 <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
141 <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
142 <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
143 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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144 <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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145 </test>
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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diff changeset
147 <param name="selected_algorithm" value="SelectKBest"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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148 <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
149 <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
150 <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
151 <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
152 <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
153 <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
154 <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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155 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
156 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
157 <param name="selected_algorithm" value="SelectFpr"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
158 <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
159 <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
160 <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
161 <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
162 <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
163 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
164 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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165 <output name="outfile" file="feature_selection_result05"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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166 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
167 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
168 <param name="selected_algorithm" value="SelectFdr"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
169 <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
170 <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
171 <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
172 <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
173 <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
174 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
175 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
176 <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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177 </test>
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
parents:
diff changeset
179 <param name="selected_algorithm" value="SelectFwe"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
180 <param name="alpha" value="0.05"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
181 <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
182 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
183 <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
184 <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
185 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
186 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
187 <output name="outfile" file="feature_selection_result07"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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188 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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189 <test>
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190 <param name="selected_algorithm" value="RFE"/>
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191 <param name="input_mode" value="new"/>
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192 <param name="selected_module" value="ensemble"/>
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193 <param name="selected_estimator" value="RandomForestRegressor"/>
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194 <param name="text_params" value="n_estimators=10, random_state=10"/>
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195 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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196 <param name="header1" value="false"/>
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197 <param name="col1" value="1,2,3,4,5"/>
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198 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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199 <param name="col2" value="6"/>
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200 <param name="header2" value="false"/>
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201 <output name="outfile" file="feature_selection_result08"/>
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202 </test>
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203 <test>
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204 <param name="selected_algorithm" value="RFECV"/>
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205 <param name="input_mode" value="new"/>
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206 <param name="selected_module" value="ensemble"/>
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207 <param name="selected_estimator" value="RandomForestRegressor"/>
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208 <param name="text_params" value="n_estimators=10, random_state=10"/>
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209 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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210 <param name="header1" value="false"/>
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211 <param name="col1" value="1,2,3,4,5"/>
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212 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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213 <param name="col2" value="6"/>
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214 <param name="header2" value="false"/>
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215 <output name="outfile" file="feature_selection_result09"/>
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216 </test>
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217 <test>
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218 <param name="selected_algorithm" value="VarianceThreshold"/>
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219 <param name="threshold" value="0.1"/>
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220 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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221 <param name="header1" value="True"/>
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222 <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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223 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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224 <param name="col2" value="1"/>
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225 <param name="header2" value="True"/>
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226 <output name="outfile" file="feature_selection_result10"/>
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227 </test>
6
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228 <test>
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229 <param name="selected_algorithm" value="SelectKBest"/>
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230 <param name="k" value="3"/>
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231 <param name="infile1" value="test3.tabular" ftype="tabular"/>
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232 <param name="header1" value="True"/>
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233 <param name="selected_column_selector_option" value="all_but_by_header_name"/>
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234 <param name="col1" value="target"/>
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235 <param name="infile2" value="test3.tabular" ftype="tabular"/>
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236 <param name="header2" value="True"/>
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237 <param name="selected_column_selector_option2" value="by_header_name"/>
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238 <param name="col2" value="target"/>
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239 <output name="outfile" file="feature_selection_result11"/>
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240 </test>
10
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241 <test>
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242 <param name="selected_algorithm" value="SelectFromModel"/>
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243 <param name="input_mode" value="prefitted"/>
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244 <param name="fitted_estimator" value="rfr_model01" ftype="zip"/>
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245 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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246 <param name="header1" value="false"/>
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247 <param name="col1" value="1,2,3,4,5"/>
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248 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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249 <param name="col2" value="1"/>
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250 <param name="header2" value="false"/>
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251 <output name="outfile" file="feature_selection_result12"/>
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252 </test>
0
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253 </tests>
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254 <help>
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255 <![CDATA[
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256 **What it does**
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257 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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258 sklearn.metrics package.
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259 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
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260
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261 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
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262 ]]>
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263 </help>
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264 <expand macro="sklearn_citation"/>
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265 </tool>