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comparison main_macros.xml @ 24:abb5a3f256e3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
author bgruening
date Tue, 14 May 2019 18:11:02 -0400
parents 9d234733ccfd
children 27903ce9b4be
comparison
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23:9d234733ccfd 24:abb5a3f256e3
1 <macros> 1 <macros>
2 <token name="@VERSION@">1.0</token> 2 <token name="@VERSION@">1.0.0.4</token>
3 3
4 <xml name="python_requirements"> 4 <xml name="python_requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="3.6">python</requirement> 6 <requirement type="package" version="3.6">python</requirement>
7 <requirement type="package" version="0.20.2">scikit-learn</requirement> 7 <requirement type="package" version="0.20.3">scikit-learn</requirement>
8 <requirement type="package" version="0.23.4">pandas</requirement> 8 <requirement type="package" version="0.24.2">pandas</requirement>
9 <requirement type="package" version="0.80">xgboost</requirement> 9 <requirement type="package" version="0.80">xgboost</requirement>
10 <requirement type="package" version="0.9.13">asteval</requirement> 10 <requirement type="package" version="0.9.13">asteval</requirement>
11 <yield /> 11 <requirement type="package" version="0.6">skrebate</requirement>
12 <requirement type="package" version="0.4.2">imbalanced-learn</requirement>
13 <requirement type="package" version="0.16.0">mlxtend</requirement>
14 <yield/>
12 </requirements> 15 </requirements>
13 </xml> 16 </xml>
14 17
15 <xml name="macro_stdio"> 18 <xml name="macro_stdio">
16 <stdio> 19 <stdio>
350 <option value="by_header_name">Select columns by column header name(s)</option> 353 <option value="by_header_name">Select columns by column header name(s)</option>
351 <option value="all_but_by_header_name">All columns BUT by column header name(s)</option> 354 <option value="all_but_by_header_name">All columns BUT by column header name(s)</option>
352 <option value="all_columns">All columns</option> 355 <option value="all_columns">All columns</option>
353 </param> 356 </param>
354 <when value="by_index_number"> 357 <when value="by_index_number">
355 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" data_ref="@INFILE@" label="Select target column(s):"/> 358 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" use_header_names="true" data_ref="@INFILE@" label="Select target column(s):"/>
356 </when> 359 </when>
357 <when value="all_but_by_index_number"> 360 <when value="all_but_by_index_number">
358 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" data_ref="@INFILE@" label="Select target column(s):"/> 361 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" use_header_names="true" data_ref="@INFILE@" label="Select target column(s):"/>
359 </when> 362 </when>
360 <when value="by_header_name"> 363 <when value="by_header_name">
361 <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="Comma-separated string. For example: target1,target2"/> 364 <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="Comma-separated string. For example: target1,target2"/>
362 </when> 365 </when>
363 <when value="all_but_by_header_name"> 366 <when value="all_but_by_header_name">
426 <param name="selected_input" type="select" label="Select input type:"> 429 <param name="selected_input" type="select" label="Select input type:">
427 <option value="tabular" selected="true">tabular data</option> 430 <option value="tabular" selected="true">tabular data</option>
428 <option value="sparse">sparse matrix</option> 431 <option value="sparse">sparse matrix</option>
429 </param> 432 </param>
430 <when value="tabular"> 433 <when value="tabular">
431 <expand macro="samples_tabular" multiple1="true"/> 434 <expand macro="samples_tabular" multiple1="true" multiple2="false"/>
432 </when> 435 </when>
433 <when value="sparse"> 436 <when value="sparse">
434 <expand macro="sparse_target"/> 437 <expand macro="sparse_target"/>
435 </when> 438 </when>
436 </conditional> 439 </conditional>
821 <option value="RepeatedStratifiedKFold">RepeatedStratifiedKFold</option> 824 <option value="RepeatedStratifiedKFold">RepeatedStratifiedKFold</option>
822 <option value="ShuffleSplit">ShuffleSplit</option> 825 <option value="ShuffleSplit">ShuffleSplit</option>
823 <option value="StratifiedShuffleSplit">StratifiedShuffleSplit</option> 826 <option value="StratifiedShuffleSplit">StratifiedShuffleSplit</option>
824 <option value="TimeSeriesSplit">TimeSeriesSplit</option> 827 <option value="TimeSeriesSplit">TimeSeriesSplit</option>
825 <option value="PredefinedSplit">PredefinedSplit</option> 828 <option value="PredefinedSplit">PredefinedSplit</option>
829 <option value="OrderedKFold">OrderedKFold</option>
830 <option value="RepeatedOrderedKFold">RepeatedOrderedKFold</option>
826 <yield/> 831 <yield/>
827 </xml> 832 </xml>
828 833
829 <xml name="cv_splitter_options"> 834 <xml name="cv_splitter_options">
830 <when value="default"> 835 <when value="default">
869 <expand macro="cv_n_splits"/> 874 <expand macro="cv_n_splits"/>
870 <param argument="max_train_size" type="integer" value="" optional="true" label="Maximum size of the training set" help="Maximum size for a single training set." /> 875 <param argument="max_train_size" type="integer" value="" optional="true" label="Maximum size of the training set" help="Maximum size for a single training set." />
871 </when> 876 </when>
872 <when value="PredefinedSplit"> 877 <when value="PredefinedSplit">
873 <param argument="test_fold" type="text" value="" area="true" label="test_fold" help="List, e.g., [0, 1, -1, 1], represents two test sets, [X[0]] and [X[1], X[3]], X[2] is excluded from any test set due to '-1'."/> 878 <param argument="test_fold" type="text" value="" area="true" label="test_fold" help="List, e.g., [0, 1, -1, 1], represents two test sets, [X[0]] and [X[1], X[3]], X[2] is excluded from any test set due to '-1'."/>
879 </when>
880 <when value="OrderedKFold">
881 <expand macro="cv_n_splits"/>
882 <expand macro="cv_shuffle"/>
883 <expand macro="random_state"/>
884 </when>
885 <when value="RepeatedOrderedKFold">
886 <expand macro="cv_n_splits"/>
887 <param argument="n_repeats" type="integer" value="5"/>
888 <expand macro="random_state"/>
874 </when> 889 </when>
875 <yield/> 890 <yield/>
876 </xml> 891 </xml>
877 892
878 <xml name="cv"> 893 <xml name="cv">
927 <xml name="cv_test_size" token_value="0.2"> 942 <xml name="cv_test_size" token_value="0.2">
928 <param argument="test_size" type="float" value="@VALUE@" min="0.0" label="Portion or number of the test set" help="0.0-1.0, proportion of the dataset to include in the test split; >1, integer only, the absolute number of test samples "/> 943 <param argument="test_size" type="float" value="@VALUE@" min="0.0" label="Portion or number of the test set" help="0.0-1.0, proportion of the dataset to include in the test split; >1, integer only, the absolute number of test samples "/>
929 </xml> 944 </xml>
930 945
931 <xml name="cv_groups" > 946 <xml name="cv_groups" >
932 <param argument="groups" type="text" value="" area="true" label="Groups" help="Group lables in a list. e.g., [1, 1, 2, 2, 3, 3, 3]"/> 947 <section name="groups_selector" title="Groups column selector" expanded="true">
948 <param name="infile_g" type="data" format="tabular" label="Choose dataset containing groups info:"/>
949 <param name="header_g" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
950 <conditional name="column_selector_options_g">
951 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option_g" col_name="col_g" multiple="False" infile="infile_g"/>
952 </conditional>
953 </section>
933 </xml> 954 </xml>
934 955
935 <xml name="feature_selection_algorithms"> 956 <xml name="feature_selection_algorithms">
936 <option value="SelectKBest" selected="true">SelectKBest - Select features according to the k highest scores</option> 957 <option value="SelectKBest" selected="true">SelectKBest - Select features according to the k highest scores</option>
937 <option value="GenericUnivariateSelect">GenericUnivariateSelect - Univariate feature selector with configurable strategy</option> 958 <option value="GenericUnivariateSelect">GenericUnivariateSelect - Univariate feature selector with configurable strategy</option>
941 <option value="SelectFwe">SelectFwe - Filter: Select the p-values corresponding to Family-wise error rate</option> 962 <option value="SelectFwe">SelectFwe - Filter: Select the p-values corresponding to Family-wise error rate</option>
942 <option value="VarianceThreshold">VarianceThreshold - Feature selector that removes all low-variance features</option> 963 <option value="VarianceThreshold">VarianceThreshold - Feature selector that removes all low-variance features</option>
943 <option value="SelectFromModel">SelectFromModel - Meta-transformer for selecting features based on importance weights</option> 964 <option value="SelectFromModel">SelectFromModel - Meta-transformer for selecting features based on importance weights</option>
944 <option value="RFE">RFE - Feature ranking with recursive feature elimination</option> 965 <option value="RFE">RFE - Feature ranking with recursive feature elimination</option>
945 <option value="RFECV">RFECV - Feature ranking with recursive feature elimination and cross-validated selection of the best number of features</option> 966 <option value="RFECV">RFECV - Feature ranking with recursive feature elimination and cross-validated selection of the best number of features</option>
967 <yield/>
946 </xml> 968 </xml>
947 969
948 <xml name="feature_selection_algorithm_details"> 970 <xml name="feature_selection_algorithm_details">
949 <when value="GenericUnivariateSelect"> 971 <when value="GenericUnivariateSelect">
950 <expand macro="feature_selection_score_function" /> 972 <expand macro="feature_selection_score_function" />
989 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep."/> 1011 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep."/>
990 </section> 1012 </section>
991 </when> 1013 </when>
992 <when value="VarianceThreshold"> 1014 <when value="VarianceThreshold">
993 <section name="options" title="Options" expanded="False"> 1015 <section name="options" title="Options" expanded="False">
994 <param argument="threshold" type="float" value="" optional="True" label="Threshold" help="Features with a training-set variance lower than this threshold will be removed."/> 1016 <param argument="threshold" type="float" value="0.0" optional="True" label="Threshold" help="Features with a training-set variance lower than this threshold will be removed."/>
995 </section> 1017 </section>
996 </when> 1018 </when>
997 </xml> 1019 </xml>
998 1020
999 <xml name="feature_selection_SelectFromModel"> 1021 <xml name="feature_selection_SelectFromModel">
1045 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." /> 1067 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
1046 </section> 1068 </section>
1047 </when> 1069 </when>
1048 </xml> 1070 </xml>
1049 1071
1050 <xml name="feature_selection_RFECV"> 1072 <xml name="feature_selection_RFECV_fs">
1073 <when value="RFECV">
1074 <yield/>
1075 <section name="options" title="Advanced Options" expanded="False">
1076 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " />
1077 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected"/>
1078 <expand macro="cv"/>
1079 <expand macro="scoring_selection"/>
1080 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
1081 </section>
1082 </when>
1083 </xml>
1084
1085 <xml name="feature_selection_RFECV_pipeline">
1051 <when value="RFECV"> 1086 <when value="RFECV">
1052 <yield/> 1087 <yield/>
1053 <section name="options" title="Advanced Options" expanded="False"> 1088 <section name="options" title="Advanced Options" expanded="False">
1054 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " /> 1089 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " />
1055 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected"/> 1090 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected"/>
1056 <expand macro="cv_reduced"/> 1091 <expand macro="cv_reduced"/>
1092 <!-- TODO: group splitter support-->
1057 <expand macro="scoring_selection"/> 1093 <expand macro="scoring_selection"/>
1058 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." /> 1094 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
1059 </section> 1095 </section>
1060 </when> 1096 </when>
1061 </xml> 1097 </xml>
1062 1098
1099 <xml name="feature_selection_DyRFECV_fs">
1100 <when value="DyRFECV">
1101 <yield/>
1102 <section name="options" title="Advanced Options" expanded="False">
1103 <param argument="step" type="text" size="30" value="1" label="step" optional="true" help="Default = 1. Support float, int and list." >
1104 <sanitizer>
1105 <valid initial="default">
1106 <add value="["/>
1107 <add value="]"/>
1108 </valid>
1109 </sanitizer>
1110 </param>
1111 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected"/>
1112 <expand macro="cv"/>
1113 <expand macro="scoring_selection"/>
1114 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
1115 </section>
1116 </when>
1117 </xml>
1118
1063 <xml name="feature_selection_pipeline"> 1119 <xml name="feature_selection_pipeline">
1064 <!--compare to `feature_selection_fs`, no fitted estimator for SelectFromModel and no customer estimator for RFE and RFECV--> 1120 <!--compare to `feature_selection_fs`, no fitted estimator for SelectFromModel and no custom estimator for RFE and RFECV-->
1065 <conditional name="fs_algorithm_selector"> 1121 <conditional name="fs_algorithm_selector">
1066 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm"> 1122 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm">
1067 <expand macro="feature_selection_algorithms"/> 1123 <expand macro="feature_selection_algorithms"/>
1068 </param> 1124 </param>
1069 <expand macro="feature_selection_algorithm_details"/> 1125 <expand macro="feature_selection_algorithm_details"/>
1070 <expand macro="feature_selection_SelectFromModel_no_prefitted"/> 1126 <expand macro="feature_selection_SelectFromModel_no_prefitted"/>
1071 <expand macro="feature_selection_RFE"> 1127 <expand macro="feature_selection_RFE">
1072 <expand macro="estimator_selector_all"/> 1128 <expand macro="estimator_selector_all"/>
1073 </expand> 1129 </expand>
1074 <expand macro="feature_selection_RFECV"> 1130 <expand macro="feature_selection_RFECV_pipeline">
1075 <expand macro="estimator_selector_all"/> 1131 <expand macro="estimator_selector_all"/>
1076 </expand> 1132 </expand>
1133 <!-- TODO: add DyRFECV to pipeline-->
1077 </conditional> 1134 </conditional>
1078 </xml> 1135 </xml>
1079 1136
1080 <xml name="feature_selection_fs"> 1137 <xml name="feature_selection_fs">
1081 <conditional name="fs_algorithm_selector"> 1138 <conditional name="fs_algorithm_selector">
1082 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm"> 1139 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm">
1083 <expand macro="feature_selection_algorithms"/> 1140 <expand macro="feature_selection_algorithms">
1141 <option value="DyRFECV">DyRFECV - Extended RFECV with changeable steps</option>
1142 </expand>
1084 </param> 1143 </param>
1085 <expand macro="feature_selection_algorithm_details"/> 1144 <expand macro="feature_selection_algorithm_details"/>
1086 <expand macro="feature_selection_SelectFromModel"/> 1145 <expand macro="feature_selection_SelectFromModel"/>
1087 <expand macro="feature_selection_RFE"> 1146 <expand macro="feature_selection_RFE">
1088 <expand macro="estimator_selector_fs"/> 1147 <expand macro="estimator_selector_fs"/>
1089 </expand> 1148 </expand>
1090 <expand macro="feature_selection_RFECV"> 1149 <expand macro="feature_selection_RFECV_fs">
1150 <expand macro="estimator_selector_fs"/>
1151 </expand>
1152 <expand macro="feature_selection_DyRFECV_fs">
1091 <expand macro="estimator_selector_fs"/> 1153 <expand macro="estimator_selector_fs"/>
1092 </expand> 1154 </expand>
1093 </conditional> 1155 </conditional>
1094 </xml> 1156 </xml>
1095 1157
1103 </param> 1165 </param>
1104 </xml> 1166 </xml>
1105 1167
1106 <xml name="model_validation_common_options"> 1168 <xml name="model_validation_common_options">
1107 <expand macro="cv"/> 1169 <expand macro="cv"/>
1108 <expand macro="verbose"/> 1170 <!-- expand macro="verbose"/> -->
1109 <yield/> 1171 <yield/>
1110 </xml> 1172 </xml>
1111 1173
1112 <xml name="scoring_selection"> 1174 <xml name="scoring_selection">
1113 <conditional name="scoring"> 1175 <conditional name="scoring">
1137 <option value="neg_mean_absolute_error">Regression -- 'neg_mean_absolute_error'</option> 1199 <option value="neg_mean_absolute_error">Regression -- 'neg_mean_absolute_error'</option>
1138 <option value="neg_mean_squared_error">Regression -- 'neg_mean_squared_error'</option> 1200 <option value="neg_mean_squared_error">Regression -- 'neg_mean_squared_error'</option>
1139 <option value="neg_mean_squared_log_error">Regression -- 'neg_mean_squared_log_error'</option> 1201 <option value="neg_mean_squared_log_error">Regression -- 'neg_mean_squared_log_error'</option>
1140 <option value="neg_median_absolute_error">Regression -- 'neg_median_absolute_error'</option> 1202 <option value="neg_median_absolute_error">Regression -- 'neg_median_absolute_error'</option>
1141 <option value="r2">Regression -- 'r2'</option> 1203 <option value="r2">Regression -- 'r2'</option>
1204 <option value="binarize_auc_scorer">anomaly detection -- binarize_auc_scorer</option>
1205 <option value="binarize_average_precision_scorer">anomaly detection -- binarize_average_precision_scorer</option>
1142 </param> 1206 </param>
1143 <when value="default"/> 1207 <when value="default"/>
1144 <when value="accuracy"><expand macro="secondary_scoring_selection_classification"/></when> 1208 <when value="accuracy"><expand macro="secondary_scoring_selection_classification"/></when>
1145 <when value="balanced_accuracy"><expand macro="secondary_scoring_selection_classification"/></when> 1209 <when value="balanced_accuracy"><expand macro="secondary_scoring_selection_classification"/></when>
1146 <when value="average_precision"><expand macro="secondary_scoring_selection_classification"/></when> 1210 <when value="average_precision"><expand macro="secondary_scoring_selection_classification"/></when>
1165 <when value="neg_mean_absolute_error"><expand macro="secondary_scoring_selection_regression"/></when> 1229 <when value="neg_mean_absolute_error"><expand macro="secondary_scoring_selection_regression"/></when>
1166 <when value="neg_mean_squared_error"><expand macro="secondary_scoring_selection_regression"/></when> 1230 <when value="neg_mean_squared_error"><expand macro="secondary_scoring_selection_regression"/></when>
1167 <when value="neg_mean_squared_log_error"><expand macro="secondary_scoring_selection_regression"/></when> 1231 <when value="neg_mean_squared_log_error"><expand macro="secondary_scoring_selection_regression"/></when>
1168 <when value="neg_median_absolute_error"><expand macro="secondary_scoring_selection_regression"/></when> 1232 <when value="neg_median_absolute_error"><expand macro="secondary_scoring_selection_regression"/></when>
1169 <when value="r2"><expand macro="secondary_scoring_selection_regression"/></when> 1233 <when value="r2"><expand macro="secondary_scoring_selection_regression"/></when>
1234 <when value="binarize_auc_scorer"><expand macro="secondary_scoring_selection_anormaly"/></when>
1235 <when value="binarize_average_precision_scorer"><expand macro="secondary_scoring_selection_anormaly"/></when>
1170 </conditional> 1236 </conditional>
1171 </xml> 1237 </xml>
1172 1238
1173 <xml name="secondary_scoring_selection_classification"> 1239 <xml name="secondary_scoring_selection_classification">
1174 <param name="secondary_scoring" type="select" multiple="true" label="Additional scoring used in multi-metric mode:" help="If the same metric with the primary is chosen, the metric will be ignored."> 1240 <param name="secondary_scoring" type="select" multiple="true" label="Additional scoring used in multi-metric mode:" help="If the same metric with the primary is chosen, the metric will be ignored.">
1204 <option value="neg_median_absolute_error">Regression -- 'neg_median_absolute_error'</option> 1270 <option value="neg_median_absolute_error">Regression -- 'neg_median_absolute_error'</option>
1205 <option value="r2">Regression -- 'r2'</option> 1271 <option value="r2">Regression -- 'r2'</option>
1206 </param> 1272 </param>
1207 </xml> 1273 </xml>
1208 1274
1275 <xml name="secondary_scoring_selection_anormaly">
1276 <param name="secondary_scoring" type="select" multiple="true" label="Additional scoring used in multi-metric mode:" help="If the same metric with the primary is chosen, the metric will be ignored.">
1277 <option value="binarize_auc_scorer">anomaly detection -- binarize_auc_scorer</option>
1278 <option value="binarize_average_precision_scorer">anomaly detection -- binarize_average_precision_scorer</option>
1279 </param>
1280 </xml>
1281
1209 <xml name="pre_dispatch" token_type="hidden" token_default_value="all" token_help="Number of predispatched jobs for parallel execution"> 1282 <xml name="pre_dispatch" token_type="hidden" token_default_value="all" token_help="Number of predispatched jobs for parallel execution">
1210 <param argument="pre_dispatch" type="@TYPE@" value="@DEFAULT_VALUE@" optional="true" label="pre_dispatch" help="@HELP@"/> 1283 <param argument="pre_dispatch" type="@TYPE@" value="@DEFAULT_VALUE@" optional="true" label="pre_dispatch" help="@HELP@"/>
1211 </xml> 1284 </xml>
1212 1285
1213 <xml name="search_cv_estimator"> 1286 <xml name="search_cv_estimator">
1214 <param name="infile_pipeline" type="data" format="zip" label="Choose the dataset containing pipeline object:"/> 1287 <param name="infile_estimator" type="data" format="zip" label="Choose the dataset containing pipeline/estimator object"/>
1215 <section name="search_params_builder" title="Search parameters Builder" expanded="true"> 1288 <section name="search_params_builder" title="Search parameters Builder" expanded="true">
1216 <repeat name="param_set" min="1" max="20" title="Parameter setting for search:"> 1289 <param name="infile_params" type="data" format="tabular" label="Choose the dataset containing parameter names"/>
1217 <conditional name="search_param_selector"> 1290 <repeat name="param_set" min="1" max="30" title="Parameter settings for search:">
1218 <param name="selected_param_type" type="select" label="Choose the transformation the parameter belongs to"> 1291 <param name="sp_name" type="select" label="Choose a parameter name (with current value)">
1219 <option value="final_estimator_p" selected="true">Final estimator</option> 1292 <options from_dataset="infile_params" startswith="@">
1220 <option value="prep_1_p">Pre-processing step #1</option> 1293 <column name="name" index="2"/>
1221 <option value="prep_2_p">Pre-processing step #2</option> 1294 <column name="value" index="1"/>
1222 <option value="prep_3_p">Pre-processing step #3</option> 1295 <filter type="unique_value" name="unique_param" column="1"/>
1223 <option value="prep_4_p">Pre-processing step #4</option> 1296 <filter type="sort_by" name="sorted_param" column="2"/>
1224 <option value="prep_5_p">Pre-processing step #5</option> 1297 </options>
1225 </param> 1298 </param>
1226 <when value="final_estimator_p"> 1299 <param name="sp_list" type="text" value="" optional="true" label="Search list" help="list or array-like, for example: [1, 10, 100, 1000], [True, False] and ['auto', 'sqrt', None]. See `help` section for more examples">
1227 <expand macro="search_param_input" /> 1300 <sanitizer>
1228 </when> 1301 <valid initial="default">
1229 <when value="prep_1_p"> 1302 <add value="&apos;"/>
1230 <expand macro="search_param_input" label="Pre_processing component #1 parameter:" help="One parameter per box. For example: with_centering: [True, False]."/> 1303 <add value="&quot;"/>
1231 </when> 1304 <add value="["/>
1232 <when value="prep_2_p"> 1305 <add value="]"/>
1233 <expand macro="search_param_input" label="Pre_processing component #2 parameter:" help="One parameter per box. For example: k: [3, 5, 7, 9]. See bottom for more examples"/> 1306 </valid>
1234 </when> 1307 </sanitizer>
1235 <when value="prep_3_p"> 1308 </param>
1236 <expand macro="search_param_input" label="Pre_processing component #3 parameter:" help="One parameter per box. For example: n_components: [1, 10, 100, 1000]. See bottom for more examples"/>
1237 </when>
1238 <when value="prep_4_p">
1239 <expand macro="search_param_input" label="Pre_processing component #4 parameter:" help="One parameter per box. For example: n_components: [1, 10, 100, 1000]. See bottom for more examples"/>
1240 </when>
1241 <when value="prep_5_p">
1242 <expand macro="search_param_input" label="Pre_processing component #5 parameter:" help="One parameter per box. For example: affinity: ['euclidean', 'l1', 'l2', 'manhattan']. See bottom for more examples"/>
1243 </when>
1244 </conditional>
1245 </repeat> 1309 </repeat>
1246 </section> 1310 </section>
1247 </xml>
1248
1249 <xml name="search_param_input" token_label="Estimator parameter:" token_help="One parameter per box. For example: C: [1, 10, 100, 1000]. See bottom for more examples">
1250 <param name="search_p" type="text" value="" optional="true" label="@LABEL@" help="@HELP@">
1251 <sanitizer>
1252 <valid initial="default">
1253 <add value="&apos;"/>
1254 <add value="&quot;"/>
1255 <add value="["/>
1256 <add value="]"/>
1257 </valid>
1258 </sanitizer>
1259 </param>
1260 </xml> 1311 </xml>
1261 1312
1262 <xml name="search_cv_options"> 1313 <xml name="search_cv_options">
1263 <expand macro="scoring_selection"/> 1314 <expand macro="scoring_selection"/>
1264 <expand macro="model_validation_common_options"/> 1315 <expand macro="model_validation_common_options"/>
1265 <expand macro="pre_dispatch" value="2*n_jobs" help="Controls the number of jobs that get dispatched during parallel execution"/> 1316 <!--expand macro="pre_dispatch" default_value="2*n_jobs" help="Controls the number of jobs that get dispatched during parallel execution"/-->
1266 <param argument="iid" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="iid" help="If True, data is identically distributed across the folds"/> 1317 <param argument="iid" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="iid" help="If True, data is identically distributed across the folds"/>
1267 <param argument="refit" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="refit" help="Refit an estimator using the best found parameters on the whole dataset."/> 1318 <param argument="refit" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="refit" help="Refit an estimator using the best found parameters on the whole dataset."/>
1268 <param argument="error_score" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Raise fit error:" help="If false, the metric score is assigned to NaN if an error occurs in estimator fitting and FitFailedWarning is raised."/> 1319 <param argument="error_score" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Raise fit error:" help="If false, the metric score is assigned to NaN if an error occurs in estimator fitting and FitFailedWarning is raised."/>
1269 <param argument="return_train_score" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="return_train_score" help=""/> 1320 <param argument="return_train_score" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="return_train_score" help=""/>
1270 </xml> 1321 </xml>
1401 1452
1402 <xml name="estimator_selector_fs"> 1453 <xml name="estimator_selector_fs">
1403 <conditional name="estimator_selector"> 1454 <conditional name="estimator_selector">
1404 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" > 1455 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" >
1405 <expand macro="estimator_module_options"> 1456 <expand macro="estimator_module_options">
1406 <option value="customer_estimator">Load a customer estimator</option> 1457 <option value="custom_estimator">Load a custom estimator</option>
1407 </expand> 1458 </expand>
1408 </param> 1459 </param>
1409 <expand macro="estimator_suboptions"> 1460 <expand macro="estimator_suboptions">
1410 <when value="customer_estimator"> 1461 <when value="custom_estimator">
1411 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the customer estimator or pipeline:"/> 1462 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline:"/>
1412 </when> 1463 </when>
1413 </expand> 1464 </expand>
1414 </conditional> 1465 </conditional>
1415 </xml> 1466 </xml>
1416 1467
1589 <option value="over_sampling.SVMSMOTE">over_sampling.SVMSMOTE</option> 1640 <option value="over_sampling.SVMSMOTE">over_sampling.SVMSMOTE</option>
1590 <option value="over_sampling.BorderlineSMOTE">over_sampling.BorderlineSMOTE</option> 1641 <option value="over_sampling.BorderlineSMOTE">over_sampling.BorderlineSMOTE</option>
1591 <option value="over_sampling.SMOTENC">over_sampling.SMOTENC</option> 1642 <option value="over_sampling.SMOTENC">over_sampling.SMOTENC</option>
1592 <option value="combine.SMOTEENN">combine.SMOTEENN</option> 1643 <option value="combine.SMOTEENN">combine.SMOTEENN</option>
1593 <option value="combine.SMOTETomek">combine.SMOTETomek</option> 1644 <option value="combine.SMOTETomek">combine.SMOTETomek</option>
1645 <option value="Z_RandomOverSampler">Z_RandomOverSampler - for regression</option>
1594 </param> 1646 </param>
1595 <when value="under_sampling.ClusterCentroids"> 1647 <when value="under_sampling.ClusterCentroids">
1596 <expand macro="estimator_params_text" 1648 <expand macro="estimator_params_text"
1597 help="Default(=blank): sampling_strategy='auto', random_state=None, estimator=None, voting='auto'."/> 1649 help="Default(=blank): sampling_strategy='auto', random_state=None, estimator=None, voting='auto'."/>
1598 </when> 1650 </when>
1666 </when> 1718 </when>
1667 <when value="combine.SMOTETomek"> 1719 <when value="combine.SMOTETomek">
1668 <expand macro="estimator_params_text" 1720 <expand macro="estimator_params_text"
1669 help="Default(=blank): sampling_strategy='auto', random_state=None, smote=None, tomek=None."/> 1721 help="Default(=blank): sampling_strategy='auto', random_state=None, smote=None, tomek=None."/>
1670 </when> 1722 </when>
1723 <when value="Z_RandomOverSampler">
1724 <expand macro="estimator_params_text"
1725 help="Default(=blank): sampling_strategy='auto', random_state=None, negative_thres=0, positive_thres=-1."/>
1726 </when>
1727 </conditional>
1728 </xml>
1729
1730 <xml name="stacking_ensemble_inputs">
1731 <section name="options" title="Advanced Options" expanded="false">
1732 <yield/>
1733 <param argument="use_features_in_secondary" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false"/>
1734 <param argument="store_train_meta_features" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false"/>
1735 </section>
1736 </xml>
1737
1738 <xml name="stacking_base_estimator">
1739 <conditional name="estimator_selector">
1740 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" >
1741 <expand macro="estimator_module_options">
1742 <option value="custom_estimator">Load a custom estimator</option>
1743 </expand>
1744 </param>
1745 <expand macro="estimator_suboptions">
1746 <when value="custom_estimator">
1747 <param name="c_estimator" type="data" format="zip" label="Choose the dataset containing the custom estimator or pipeline"/>
1748 </when>
1749 </expand>
1671 </conditional> 1750 </conditional>
1672 </xml> 1751 </xml>
1673 1752
1674 <!-- Outputs --> 1753 <!-- Outputs -->
1675 1754