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annotate stacking_ensembles.xml @ 9:b8c92e94ac1d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
author bgruening
date Tue, 13 Apr 2021 15:49:42 +0000
parents 00819b7f2f55
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b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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1 <tool id="sklearn_stacking_ensemble_models" name="Stacking Ensembles" version="@VERSION@" profile="20.05">
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2 <description>builds stacking, voting ensemble models with numerous base options</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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b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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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 "$ENSEMBLE_VERSION"</version_command>
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9 <command>
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10 <![CDATA[
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11 #for $i, $base in enumerate($base_est_builder)
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12 #if $i == 0
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13 #if $base.estimator_selector.selected_module == 'custom_estimator'
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14 bases='${base.estimator_selector.c_estimator}';
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15 #else
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16 bases='None';
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17 #end if
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18 #elif $base.estimator_selector.selected_module == 'custom_estimator'
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19 bases="\$bases,${base.estimator_selector.c_estimator}";
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20 #else
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21 bases="\$bases,None";
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22 #end if
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23 #end for
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24 python '$__tool_directory__/stacking_ensembles.py'
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25 --inputs '$inputs'
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26 --outfile '$outfile'
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27 --bases "\$bases"
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28 #if $algo_selection.estimator_type not in ('sklearn.ensemble_VotingClassifier', 'sklearn.ensemble_VotingRegressor')
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29 #if $algo_selection.meta_estimator.estimator_selector.selected_module == 'custom_estimator'
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30 --meta '${algo_selection.meta_estimator.estimator_selector.c_estimator}'
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31 #end if
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32 #end if
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33 #if $get_params
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34 --outfile_params '$outfile_params'
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35 #end if
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36 ]]>
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37 </command>
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38 <configfiles>
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39 <inputs name="inputs" />
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40 </configfiles>
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41 <inputs>
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42 <conditional name="algo_selection">
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43 <param name="estimator_type" type="select" label="Choose the stacking ensemble type">
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44 <option value="sklearn.ensemble_VotingClassifier" selected="true">sklearn.ensemble -- VotingClassifier</option>
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45 <option value="sklearn.ensemble_VotingRegressor">sklearn.ensemble -- VotingRegressor</option>
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46 <option value="mlxtend.classifier_StackingCVClassifier">mlxtend.classifier -- StackingCVClassifier</option>
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47 <option value="mlxtend.classifier_StackingClassifier">mlxtend.classifier -- StackingClassifier</option>
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48 <option value="mlxtend.regressor_StackingCVRegressor">mlxtend.regressor -- StackingCVRegressor</option>
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49 <option value="mlxtend.regressor_StackingRegressor">mlxtend.regressor -- StackingRegressor</option>
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50 </param>
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51 <when value="sklearn.ensemble_VotingClassifier">
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52 <expand macro="stacking_voting_weights">
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53 <param argument="voting" type="select" help="If ‘hard’, uses predicted class labels for majority rule voting. Else if ‘soft’, predicts the class label based on the argmax of the sums of the predicted probabilities, which is recommended for an ensemble of well-calibrated classifiers.">
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54 <option value="hard" selected="true">hard</option>
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55 <option value="soft">soft</option>
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56 </param>
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57 <param argument="flatten_transform" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" help="" />
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58 </expand>
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59 </when>
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60 <when value="sklearn.ensemble_VotingRegressor">
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61 <expand macro="stacking_voting_weights" />
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62 </when>
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63 <when value="mlxtend.classifier_StackingCVClassifier">
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64 <expand macro="stacking_ensemble_inputs">
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65 <expand macro="cv_reduced" />
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66 <expand macro="shuffle" label="shuffle" />
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67 <expand macro="random_state" default_value="" help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data." />
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68 <param argument="use_probas" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" />
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69 </expand>
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70 <section name="meta_estimator" title="Meta Estimator" expanded="true">
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71 <expand macro="stacking_base_estimator" />
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72 </section>
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73 </when>
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74 <when value="mlxtend.classifier_StackingClassifier">
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75 <expand macro="stacking_ensemble_inputs">
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76 <param argument="use_probas" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" />
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77 <param argument="average_probas" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" />
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78 </expand>
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79 <section name="meta_estimator" title="Meta Estimator" expanded="true">
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80 <expand macro="stacking_base_estimator" />
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81 </section>
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82 </when>
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83 <when value="mlxtend.regressor_StackingCVRegressor">
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84 <expand macro="stacking_ensemble_inputs">
9
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85 <expand macro="cv_reduced" />
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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86 <!--TODO support group splitters. Hint: `groups` is a fit_param-->
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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87 <expand macro="shuffle" label="shuffle" />
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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88 <expand macro="random_state" default_value="" help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data." />
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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89 <param argument="refit" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" />
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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90 </expand>
2
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91 <section name="meta_estimator" title="Meta Estimator" expanded="true">
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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92 <expand macro="stacking_base_estimator" />
2
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93 </section>
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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94 </when>
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
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95 <when value="mlxtend.regressor_StackingRegressor">
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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96 <expand macro="stacking_ensemble_inputs">
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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97 <param argument="refit" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" />
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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98 </expand>
2
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99 <section name="meta_estimator" title="Meta Estimator" expanded="true">
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b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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100 <expand macro="stacking_base_estimator" />
2
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101 </section>
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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102 </when>
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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103 </conditional>
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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104 <repeat name="base_est_builder" min="1" max="20" title="Base Estimator">
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b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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105 <expand macro="stacking_base_estimator" />
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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106 <!--param name="base_estimator" type="data" format="zip,json" label="Select the dataset containing base estimator" help="One estimator at a time."/-->
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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107 </repeat>
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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108 <!--param name="meta_estimator" type="data" format="zip,json" label="Select the dataset containing the Meta estimator"/-->
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b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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109 <param name="get_params" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Output parameters for searchCV?" help="Optional. Tunable parameters could be obtained through `estimator_attributes` tool." />
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47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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110 </inputs>
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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111 <outputs>
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112 <data format="zip" name="outfile" label="${algo_selection.estimator_type} on ${on_string}" />
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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113 <data format="tabular" name="outfile_params" label="get_params for ${algo_selection.estimator_type}">
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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114 <filter>get_params</filter>
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115 </data>
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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116 </outputs>
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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117 <tests>
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118 <test>
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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119 <conditional name="algo_selection">
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120 <param name="estimator_type" value="sklearn.ensemble_VotingClassifier" />
2
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121 <section name="options">
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b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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122 <param name="weights" value="[1, 2]" />
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123 </section>
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
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124 </conditional>
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
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125 <repeat name="base_est_builder">
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126 <conditional name="estimator_selector">
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b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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127 <param name="selected_module" value="svm" />
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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128 <param name="selected_estimator" value="SVC" />
2
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129 </conditional>
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
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130 </repeat>
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
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131 <repeat name="base_est_builder">
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132 <conditional name="estimator_selector">
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b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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133 <param name="selected_module" value="xgboost" />
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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134 <param name="selected_estimator" value="XGBClassifier" />
2
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135 </conditional>
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
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136 </repeat>
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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137 <param name="get_params" value="false" />
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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138 <output name="outfile" file="StackingVoting03.zip" compare="sim_size" delta="5" />
2
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139 </test>
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
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140 <test>
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
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141 <conditional name="algo_selection">
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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142 <param name="estimator_type" value="mlxtend.regressor_StackingCVRegressor" />
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
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143 <section name="meta_estimator">
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
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144 <conditional name="estimator_selector">
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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145 <param name="selected_module" value="custom_estimator" />
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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146 <param name="c_estimator" value="LinearRegression01.zip" ftype="zip" />
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
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147 </conditional>
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
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148 </section>
0
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149 </conditional>
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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150 <repeat name="base_est_builder">
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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151 <conditional name="estimator_selector">
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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152 <param name="selected_module" value="custom_estimator" />
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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153 <param name="c_estimator" value="RandomForestRegressor01.zip" ftype="zip" />
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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154 </conditional>
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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155 </repeat>
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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156 <repeat name="base_est_builder">
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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157 <conditional name="estimator_selector">
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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158 <param name="selected_module" value="custom_estimator" />
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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159 <param name="c_estimator" value="XGBRegressor01.zip" ftype="zip" />
0
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160 </conditional>
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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161 </repeat>
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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162 <param name="get_params" value="false" />
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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163 <output name="outfile" file="StackingCVRegressor01.zip" compare="sim_size" delta="5" />
0
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164 </test>
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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165 <test>
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166 <conditional name="algo_selection">
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
167 <param name="estimator_type" value="mlxtend.regressor_StackingRegressor" />
2
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diff changeset
168 <section name="meta_estimator">
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169 <conditional name="estimator_selector">
9
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170 <param name="selected_module" value="svm" />
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171 <param name="selected_estimator" value="SVR" />
2
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172 </conditional>
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173 </section>
0
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174 </conditional>
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175 <repeat name="base_est_builder">
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176 <conditional name="estimator_selector">
9
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177 <param name="selected_module" value="custom_estimator" />
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178 <param name="c_estimator" value="RandomForestRegressor01.zip" ftype="zip" />
0
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179 </conditional>
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180 </repeat>
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181 <repeat name="base_est_builder">
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182 <conditional name="estimator_selector">
9
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183 <param name="selected_module" value="xgboost" />
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184 <param name="selected_estimator" value="XGBRegressor" />
0
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185 </conditional>
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186 </repeat>
9
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187 <param name="get_params" value="false" />
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188 <output name="outfile" file="StackingRegressor02.zip" compare="sim_size" delta="5" />
0
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189 </test>
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190 </tests>
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191 <help>
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192 <![CDATA[
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193 This tool wrapps Stacking Regression, also called Super Learning, in which different base algorithms train
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194 on the original dataset and predict results respectively, a second level of `metalearner` fits on the previous
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195 prediction results to ensemble a strong learner.
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196 Refer to `http://docs.h2o.ai/h2o/latest-stable/h2o-docs/data-science/stacked-ensembles.html#introduction`_.
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197
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198 .. _`http://docs.h2o.ai/h2o/latest-stable/h2o-docs/data-science/stacked-ensembles.html#introduction`:
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199 http://docs.h2o.ai/h2o/latest-stable/h2o-docs/data-science/stacked-ensembles.html#introduction
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200
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201 ]]>
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202 </help>
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203 <expand macro="sklearn_citation">
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204 <expand macro="skrebate_citation" />
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205 <expand macro="xgboost_citation" />
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206 <expand macro="imblearn_citation" />
0
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207 <citation type="bibtex">
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208 @article{raschkas_2018_mlxtend,
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209 author = {Sebastian Raschka},
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210 title = {MLxtend: Providing machine learning and data science
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211 utilities and extensions to Python’s
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212 scientific computing stack},
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213 journal = {The Journal of Open Source Software},
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214 volume = {3},
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215 number = {24},
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216 month = apr,
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217 year = 2018,
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218 publisher = {The Open Journal},
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219 doi = {10.21105/joss.00638},
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220 url = {http://joss.theoj.org/papers/10.21105/joss.00638}
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221 }
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222 </citation>
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223 </expand>
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224 </tool>