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annotate feature_selection.xml @ 16:328a8d547ca2 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c64ccc5850c8e061a95fb64e07ed388384e82393
author bgruening
date Thu, 11 Oct 2018 03:34:39 -0400
parents 026667802750
children 2bbbac61e48d
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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 with open("$__tool_directory__/sk_whitelist.json", "r") as f:
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25 sk_whitelist = json.load(f)
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26 exec(open("$__tool_directory__/utils.py").read(), globals())
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28 safe_eval = SafeEval()
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29
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30 input_json_path = sys.argv[1]
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31 with open(input_json_path, "r") as param_handler:
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32 params = json.load(param_handler)
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33
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34 #handle cheetah
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35 #if $fs_algorithm_selector.selected_algorithm == "SelectFromModel"\
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36 and $fs_algorithm_selector.model_inputter.input_mode == "prefitted":
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37 params['fs_algorithm_selector']['model_inputter']['fitted_estimator'] =\
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38 "$fs_algorithm_selector.model_inputter.fitted_estimator"
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39 #end if
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40
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41 # Read features
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42 features_has_header = params["input_options"]["header1"]
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43 input_type = params["input_options"]["selected_input"]
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44 if input_type=="tabular":
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45 header = 'infer' if features_has_header else None
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46 column_option = params["input_options"]["column_selector_options_1"]["selected_column_selector_option"]
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47 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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48 c = params["input_options"]["column_selector_options_1"]["col1"]
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49 else:
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50 c = None
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51 X, input_df = read_columns(
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52 "$input_options.infile1",
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53 c = c,
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54 c_option = column_option,
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55 return_df = True,
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56 sep='\t',
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57 header=header,
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58 parse_dates=True
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59 )
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60 else:
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61 X = mmread("$input_options.infile1")
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62
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63 # Read labels
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64 header = 'infer' if params["input_options"]["header2"] else None
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65 column_option = params["input_options"]["column_selector_options_2"]["selected_column_selector_option2"]
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66 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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67 c = params["input_options"]["column_selector_options_2"]["col2"]
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68 else:
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69 c = None
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70 y = read_columns(
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71 "$input_options.infile2",
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72 c = c,
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73 c_option = column_option,
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74 sep='\t',
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75 header=header,
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76 parse_dates=True
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77 )
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78 y=y.ravel()
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79
10
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80 # Create feature selector
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81 new_selector = feature_selector(params['fs_algorithm_selector'])
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82 if params['fs_algorithm_selector']['selected_algorithm'] != 'SelectFromModel'\
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83 or params['fs_algorithm_selector']['model_inputter']['input_mode'] != 'prefitted' :
2
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84 new_selector.fit(X, y)
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85
2
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86 ## Transform to select features
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87 selected_names = None
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88 if "$output_method_selector.selected_method" == "fit_transform":
2
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89 res = new_selector.transform(X)
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90 if features_has_header:
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91 selected_names = input_df.columns[new_selector.get_support(indices=True)]
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92 else:
10
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diff changeset
93 res = new_selector.get_support(params["output_method_selector"]["indices"])
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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94
2
2eb90e73f0d5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
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diff changeset
95 res = pandas.DataFrame(res, columns = selected_names)
0
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96 res.to_csv(path_or_buf="$outfile", sep='\t', index=False)
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97
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98
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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99 ]]>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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100 </configfile>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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101 </configfiles>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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102 <inputs>
10
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103 <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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104 <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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105 </expand>
96f9b73327f2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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diff changeset
106 <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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107 <expand macro="sl_mixed_input"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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108 </inputs>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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109 <outputs>
2
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110 <data format="tabular" name="outfile"/>
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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111 </outputs>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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112 <tests>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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113 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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114 <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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115 <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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116 <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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117 <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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diff changeset
118 <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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diff changeset
119 <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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120 <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
121 <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
122 <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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diff changeset
123 <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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124 <param name="header2" value="false"/>
0
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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125 <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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126 </test>
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127 <test>
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128 <param name="selected_algorithm" value="GenericUnivariateSelect"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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129 <param name="param" value="20"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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130 <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
131 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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132 <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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133 <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
134 <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
135 <param name="header2" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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136 <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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137 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
138 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
139 <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
140 <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
141 <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
142 <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
143 <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
144 <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
145 <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
146 <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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147 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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148 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
149 <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
150 <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
151 <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
152 <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
153 <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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parents:
diff changeset
154 <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
155 <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
156 <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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157 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
158 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents:
diff changeset
159 <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
160 <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
161 <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
162 <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
163 <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
164 <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
165 <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
166 <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
167 <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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168 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
169 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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parents:
diff changeset
170 <param name="selected_algorithm" value="SelectFdr"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
171 <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
172 <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
173 <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
174 <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
175 <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
176 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
177 <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
178 <output name="outfile" file="feature_selection_result06"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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179 </test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
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diff changeset
180 <test>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
181 <param name="selected_algorithm" value="SelectFwe"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
182 <param name="alpha" value="0.05"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
183 <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
184 <param name="header1" value="True"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
bgruening
parents:
diff changeset
185 <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
186 <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
187 <param name="col2" value="1"/>
092199a095dd planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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188 <param name="header2" value="True"/>
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189 <output name="outfile" file="feature_selection_result07"/>
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190 </test>
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191 <test>
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192 <param name="selected_algorithm" value="RFE"/>
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193 <param name="input_mode" value="new"/>
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194 <param name="selected_module" value="ensemble"/>
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195 <param name="selected_estimator" value="RandomForestRegressor"/>
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196 <param name="text_params" value="n_estimators=10, random_state=10"/>
10
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197 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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198 <param name="header1" value="false"/>
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199 <param name="col1" value="1,2,3,4,5"/>
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200 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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201 <param name="col2" value="6"/>
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202 <param name="header2" value="false"/>
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203 <output name="outfile" file="feature_selection_result08"/>
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204 </test>
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205 <test>
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206 <param name="selected_algorithm" value="RFECV"/>
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207 <param name="input_mode" value="new"/>
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208 <param name="selected_module" value="ensemble"/>
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209 <param name="selected_estimator" value="RandomForestRegressor"/>
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210 <param name="text_params" value="n_estimators=10, random_state=10"/>
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211 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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212 <param name="header1" value="false"/>
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213 <param name="col1" value="1,2,3,4,5"/>
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214 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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215 <param name="col2" value="6"/>
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216 <param name="header2" value="false"/>
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217 <output name="outfile" file="feature_selection_result09"/>
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218 </test>
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219 <test>
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220 <param name="selected_algorithm" value="VarianceThreshold"/>
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221 <param name="threshold" value="0.1"/>
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222 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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223 <param name="header1" value="True"/>
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224 <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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225 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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226 <param name="col2" value="1"/>
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227 <param name="header2" value="True"/>
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228 <output name="outfile" file="feature_selection_result10"/>
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229 </test>
6
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230 <test>
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231 <param name="selected_algorithm" value="SelectKBest"/>
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232 <param name="k" value="3"/>
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233 <param name="infile1" value="test3.tabular" ftype="tabular"/>
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234 <param name="header1" value="True"/>
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235 <param name="selected_column_selector_option" value="all_but_by_header_name"/>
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236 <param name="col1" value="target"/>
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237 <param name="infile2" value="test3.tabular" ftype="tabular"/>
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238 <param name="header2" value="True"/>
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239 <param name="selected_column_selector_option2" value="by_header_name"/>
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240 <param name="col2" value="target"/>
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241 <output name="outfile" file="feature_selection_result11"/>
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242 </test>
10
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243 <test>
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244 <param name="selected_algorithm" value="SelectFromModel"/>
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245 <param name="input_mode" value="prefitted"/>
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246 <param name="fitted_estimator" value="rfr_model01" ftype="zip"/>
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247 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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248 <param name="header1" value="false"/>
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249 <param name="col1" value="1,2,3,4,5"/>
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250 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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251 <param name="col2" value="1"/>
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252 <param name="header2" value="false"/>
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253 <output name="outfile" file="feature_selection_result12"/>
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254 </test>
0
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255 </tests>
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256 <help>
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257 <![CDATA[
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258 **What it does**
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259 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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260 sklearn.metrics package.
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261 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
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262
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263 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
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264 ]]>
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265 </help>
14
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266 <expand macro="sklearn_citation">
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267 <expand macro="skrebate_citation"/>
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268 <expand macro="xgboost_citation"/>
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269 </expand>
0
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270 </tool>