Mercurial > repos > bgruening > sklearn_feature_selection

annotate feature_selection.xml @ 11:0cd9e541bf7c draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977
author bgruening
date Sat, 04 Aug 2018 17:31:14 -0400
parents d00e89558c18
children 467550472f7d
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1 <tool id="sklearn_feature_selection" name="Feature Selection" version="@VERSION@.1">
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2 <description>module, including univariate filter selection methods and recursive feature elimination algorithm</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 </macros>
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6 <expand macro="python_requirements"/>
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7 <expand macro="macro_stdio"/>
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8 <version_command>echo "@VERSION@"</version_command>
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9 <command>
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10 <![CDATA[
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11 python "$feature_selection_script" '$inputs'
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12 ]]>
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13 </command>
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14 <configfiles>
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15 <inputs name="inputs" />
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16 <configfile name="feature_selection_script">
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17 <![CDATA[
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18 import sys
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19 import json
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20 import pandas
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21 import pickle
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22 import ast
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23 import numpy as np
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24 import xgboost
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25 import sklearn.feature_selection
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26 from sklearn import svm, linear_model, ensemble, naive_bayes, tree, neighbors
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27
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28 @COLUMNS_FUNCTION@
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29 @GET_ESTIMATOR_FUNCTION@
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30 @FEATURE_SELECTOR_FUNCTION@
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31
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32 input_json_path = sys.argv[1]
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33 with open(input_json_path, "r") as param_handler:
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34 params = json.load(param_handler)
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35
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36 #handle cheetah
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37 #if $fs_algorithm_selector.selected_algorithm == "SelectFromModel"\
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38 and $fs_algorithm_selector.model_inputter.input_mode == "prefitted":
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39 params['fs_algorithm_selector']['model_inputter']['fitted_estimator'] =\
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40 "$fs_algorithm_selector.model_inputter.fitted_estimator"
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41 #end if
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42
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43 # Read features
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44 features_has_header = params["input_options"]["header1"]
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45 input_type = params["input_options"]["selected_input"]
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46 if input_type=="tabular":
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47 header = 'infer' if features_has_header else None
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48 column_option = params["input_options"]["column_selector_options_1"]["selected_column_selector_option"]
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49 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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50 c = params["input_options"]["column_selector_options_1"]["col1"]
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51 else:
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52 c = None
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53 X, input_df = read_columns(
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54 "$input_options.infile1",
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55 c = c,
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56 c_option = column_option,
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57 return_df = True,
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58 sep='\t',
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59 header=header,
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60 parse_dates=True
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61 )
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62 else:
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63 X = mmread("$input_options.infile1")
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64
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65 # Read labels
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66 header = 'infer' if params["input_options"]["header2"] else None
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67 column_option = params["input_options"]["column_selector_options_2"]["selected_column_selector_option2"]
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68 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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69 c = params["input_options"]["column_selector_options_2"]["col2"]
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70 else:
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71 c = None
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72 y = read_columns(
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73 "$input_options.infile2",
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74 c = c,
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75 c_option = column_option,
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76 sep='\t',
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77 header=header,
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78 parse_dates=True
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79 )
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80 y=y.ravel()
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81
10
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82 # Create feature selector
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83 new_selector = feature_selector(params['fs_algorithm_selector'])
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84 if params['fs_algorithm_selector']['selected_algorithm'] != 'SelectFromModel'\
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85 or params['fs_algorithm_selector']['model_inputter']['input_mode'] != 'prefitted' :
2
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86 new_selector.fit(X, y)
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87
2
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88 ## Transform to select features
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89 selected_names = None
10
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90 if "$output_method_selector.selected_method" == "fit_transform":
2
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91 res = new_selector.transform(X)
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92 if features_has_header:
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93 selected_names = input_df.columns[new_selector.get_support(indices=True)]
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94 else:
10
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95 res = new_selector.get_support(params["output_method_selector"]["indices"])
0
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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96
2
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97 res = pandas.DataFrame(res, columns = selected_names)
0
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98 res.to_csv(path_or_buf="$outfile", sep='\t', index=False)
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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99
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100
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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101 ]]>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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102 </configfile>
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103 </configfiles>
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104 <inputs>
10
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105 <expand macro="feature_selection_all">
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106 <expand macro="fs_selectfrommodel_prefitted"/>
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107 </expand>
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108 <expand macro="feature_selection_output_mothods" />
0
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109 <expand macro="sl_mixed_input"/>
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110 </inputs>
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111 <outputs>
2
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112 <data format="tabular" name="outfile"/>
0
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113 </outputs>
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114 <tests>
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115 <test>
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116 <param name="selected_algorithm" value="SelectFromModel"/>
10
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117 <param name="input_mode" value="new"/>
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118 <param name="selected_module" value="ensemble"/>
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119 <param name="selected_estimator" value="RandomForestRegressor"/>
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120 <param name="text_params" value="'n_estimators': 10, 'random_state': 10"/>
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121 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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122 <param name="header1" value="false"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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123 <param name="col1" value="1,2,3,4,5"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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124 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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125 <param name="col2" value="6"/>
d00e89558c18 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd
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126 <param name="header2" value="false"/>
0
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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127 <output name="outfile" file="feature_selection_result01"/>
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128 </test>
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129 <test>
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130 <param name="selected_algorithm" value="GenericUnivariateSelect"/>
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131 <param name="param" value="20"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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132 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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133 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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134 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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135 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
136 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
137 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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138 <output name="outfile" file="feature_selection_result02"/>
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139 </test>
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140 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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141 <param name="selected_algorithm" value="SelectPercentile"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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142 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
143 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
144 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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145 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
146 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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147 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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148 <output name="outfile" file="feature_selection_result03"/>
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149 </test>
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150 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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151 <param name="selected_algorithm" value="SelectKBest"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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152 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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153 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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154 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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155 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
156 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
157 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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158 <output name="outfile" file="feature_selection_result04"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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159 </test>
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160 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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161 <param name="selected_algorithm" value="SelectFpr"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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162 <param name="alpha" value="0.05"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
163 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
164 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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165 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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166 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
167 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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168 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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169 <output name="outfile" file="feature_selection_result05"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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170 </test>
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171 <test>
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172 <param name="selected_algorithm" value="SelectFdr"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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173 <param name="alpha" value="0.05"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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174 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
175 <param name="header1" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
176 <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
177 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
178 <param name="col2" value="1"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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179 <param name="header2" value="True"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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180 <output name="outfile" file="feature_selection_result06"/>
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181 </test>
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182 <test>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
183 <param name="selected_algorithm" value="SelectFwe"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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diff changeset
184 <param name="alpha" value="0.05"/>
2bbacfaadb5c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 7a31960686122d7e53054fef4996525f04ebd254
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185 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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186 <param name="header1" value="True"/>
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187 <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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188 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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189 <param name="col2" value="1"/>
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190 <param name="header2" value="True"/>
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191 <output name="outfile" file="feature_selection_result07"/>
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192 </test>
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193 <test>
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194 <param name="selected_algorithm" value="RFE"/>
10
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195 <param name="input_mode" value="new"/>
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196 <param name="selected_module" value="ensemble"/>
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197 <param name="selected_estimator" value="RandomForestRegressor"/>
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198 <param name="text_params" value="'n_estimators': 10, 'random_state':10"/>
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199 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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200 <param name="header1" value="false"/>
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201 <param name="col1" value="1,2,3,4,5"/>
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202 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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203 <param name="col2" value="6"/>
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204 <param name="header2" value="false"/>
0
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205 <output name="outfile" file="feature_selection_result08"/>
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206 </test>
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207 <test>
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208 <param name="selected_algorithm" value="RFECV"/>
10
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209 <param name="input_mode" value="new"/>
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210 <param name="selected_module" value="ensemble"/>
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211 <param name="selected_estimator" value="RandomForestRegressor"/>
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212 <param name="text_params" value="'n_estimators': 10, 'random_state':10"/>
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213 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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214 <param name="header1" value="false"/>
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215 <param name="col1" value="1,2,3,4,5"/>
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216 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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217 <param name="col2" value="6"/>
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218 <param name="header2" value="false"/>
0
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219 <output name="outfile" file="feature_selection_result09"/>
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220 </test>
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221 <test>
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222 <param name="selected_algorithm" value="VarianceThreshold"/>
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223 <param name="threshold" value="0.1"/>
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224 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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225 <param name="header1" value="True"/>
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226 <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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227 <param name="infile2" value="regression_y.tabular" ftype="tabular"/>
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228 <param name="col2" value="1"/>
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229 <param name="header2" value="True"/>
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230 <output name="outfile" file="feature_selection_result10"/>
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231 </test>
6
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232 <test>
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233 <param name="selected_algorithm" value="SelectKBest"/>
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234 <param name="k" value="3"/>
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235 <param name="infile1" value="test3.tabular" ftype="tabular"/>
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236 <param name="header1" value="True"/>
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237 <param name="selected_column_selector_option" value="all_but_by_header_name"/>
dc574d9778bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
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238 <param name="col1" value="target"/>
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239 <param name="infile2" value="test3.tabular" ftype="tabular"/>
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240 <param name="header2" value="True"/>
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241 <param name="selected_column_selector_option2" value="by_header_name"/>
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242 <param name="col2" value="target"/>
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243 <output name="outfile" file="feature_selection_result11"/>
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244 </test>
10
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245 <test>
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246 <param name="selected_algorithm" value="SelectFromModel"/>
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247 <param name="input_mode" value="prefitted"/>
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248 <param name="fitted_estimator" value="rfr_model01" ftype="zip"/>
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249 <param name="infile1" value="regression_train.tabular" ftype="tabular"/>
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250 <param name="header1" value="false"/>
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251 <param name="col1" value="1,2,3,4,5"/>
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252 <param name="infile2" value="regression_train.tabular" ftype="tabular"/>
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253 <param name="col2" value="1"/>
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254 <param name="header2" value="false"/>
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255 <output name="outfile" file="feature_selection_result12"/>
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256 </test>
0
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257 </tests>
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258 <help>
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259 <![CDATA[
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260 **What it does**
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261 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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262 sklearn.metrics package.
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263 For information about classification metric functions and their parameter settings please refer to `Scikit-learn classification metrics`_.
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264
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265 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
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266 ]]>
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267 </help>
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268 <expand macro="sklearn_citation"/>
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269 </tool>