Mercurial > repos > q2d2 > qiime2__feature_classifier__fit_classifier_naive_bayes
annotate qiime2__feature_classifier__fit_classifier_naive_bayes.xml @ 0:ba5db18297f6 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author | q2d2 |
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date | Mon, 29 Aug 2022 19:51:01 +0000 |
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children | 42f3a9cab210 |
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ba5db18297f6
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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1 <?xml version='1.0' encoding='utf-8'?> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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2 <!-- |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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3 Copyright (c) 2022, QIIME 2 development team. |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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4 |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) |
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6 --> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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7 <!-- |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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8 This tool was automatically generated by: |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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9 q2galaxy (version: 2022.8.1) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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10 for: |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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11 qiime2 (version: 2022.8.1) |
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12 --> |
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13 <tool name="qiime2 feature-classifier fit-classifier-naive-bayes" id="qiime2__feature_classifier__fit_classifier_naive_bayes" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> |
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14 <description>Train the naive_bayes classifier</description> |
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15 <requirements> |
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16 <container type="docker">quay.io/qiime2/core:2022.8</container> |
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17 </requirements> |
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18 <version_command>q2galaxy version feature_classifier</version_command> |
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19 <command detect_errors="aggressive">q2galaxy run feature_classifier fit_classifier_naive_bayes '$inputs'</command> |
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20 <configfiles> |
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21 <inputs name="inputs" data_style="paths"/> |
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22 </configfiles> |
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23 <inputs> |
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24 <param name="reference_reads" type="data" format="qza" label="reference_reads: FeatureData[Sequence]" help="[required]"> |
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25 <options options_filter_attribute="metadata.semantic_type"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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26 <filter type="add_value" value="FeatureData[Sequence]"/> |
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27 </options> |
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator> |
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29 </param> |
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30 <param name="reference_taxonomy" type="data" format="qza" label="reference_taxonomy: FeatureData[Taxonomy]" help="[required]"> |
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31 <options options_filter_attribute="metadata.semantic_type"> |
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32 <filter type="add_value" value="FeatureData[Taxonomy]"/> |
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33 </options> |
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34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator> |
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35 </param> |
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36 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> |
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37 <param name="class_weight" type="data" format="qza" optional="true" label="class_weight: FeatureTable[RelativeFrequency]" help="[optional]"> |
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38 <options options_filter_attribute="metadata.semantic_type"> |
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39 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> |
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40 </options> |
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41 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[RelativeFrequency]']</validator> |
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42 </param> |
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43 <param name="classify__alpha" type="float" value="0.001" label="classify__alpha: Float" help="[default: 0.001]"/> |
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44 <param name="classify__chunk_size" type="integer" value="20000" label="classify__chunk_size: Int" help="[default: 20000]"/> |
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45 <param name="classify__class_prior" type="text" value="null" label="classify__class_prior: Str" help="[default: 'null']"> |
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46 <sanitizer> |
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47 <valid initial="string.printable"/> |
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48 </sanitizer> |
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49 </param> |
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50 <param name="classify__fit_prior" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="classify__fit_prior: Bool" help="[default: No]"/> |
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51 <param name="feat_ext__alternate_sign" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="feat_ext__alternate_sign: Bool" help="[default: No]"/> |
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52 <param name="feat_ext__analyzer" type="text" value="char_wb" label="feat_ext__analyzer: Str" help="[default: 'char_wb']"> |
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53 <sanitizer> |
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54 <valid initial="string.printable"/> |
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55 </sanitizer> |
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56 </param> |
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57 <param name="feat_ext__binary" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="feat_ext__binary: Bool" help="[default: No]"/> |
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58 <param name="feat_ext__decode_error" type="text" value="strict" label="feat_ext__decode_error: Str" help="[default: 'strict']"> |
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59 <sanitizer> |
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60 <valid initial="string.printable"/> |
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61 </sanitizer> |
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62 </param> |
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63 <param name="feat_ext__encoding" type="text" value="utf-8" label="feat_ext__encoding: Str" help="[default: 'utf-8']"> |
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64 <sanitizer> |
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65 <valid initial="string.printable"/> |
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66 </sanitizer> |
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67 </param> |
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68 <param name="feat_ext__input" type="text" value="content" label="feat_ext__input: Str" help="[default: 'content']"> |
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69 <sanitizer> |
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70 <valid initial="string.printable"/> |
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71 </sanitizer> |
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72 </param> |
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73 <param name="feat_ext__lowercase" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="feat_ext__lowercase: Bool" help="[default: Yes]"/> |
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74 <param name="feat_ext__n_features" type="integer" value="8192" label="feat_ext__n_features: Int" help="[default: 8192]"/> |
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75 <param name="feat_ext__ngram_range" type="text" value="[7, 7]" label="feat_ext__ngram_range: Str" help="[default: '[7, 7]']"> |
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76 <sanitizer> |
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77 <valid initial="string.printable"/> |
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78 </sanitizer> |
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79 </param> |
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80 <param name="feat_ext__norm" type="text" value="l2" label="feat_ext__norm: Str" help="[default: 'l2']"> |
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81 <sanitizer> |
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82 <valid initial="string.printable"/> |
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83 </sanitizer> |
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84 </param> |
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85 <param name="feat_ext__preprocessor" type="text" value="null" label="feat_ext__preprocessor: Str" help="[default: 'null']"> |
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86 <sanitizer> |
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87 <valid initial="string.printable"/> |
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88 </sanitizer> |
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89 </param> |
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90 <param name="feat_ext__stop_words" type="text" value="null" label="feat_ext__stop_words: Str" help="[default: 'null']"> |
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91 <sanitizer> |
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92 <valid initial="string.printable"/> |
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93 </sanitizer> |
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94 </param> |
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95 <param name="feat_ext__strip_accents" type="text" value="null" label="feat_ext__strip_accents: Str" help="[default: 'null']"> |
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96 <sanitizer> |
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97 <valid initial="string.printable"/> |
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98 </sanitizer> |
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99 </param> |
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100 <param name="feat_ext__token_pattern" type="text" value="(?u)\b\w\w+\b" label="feat_ext__token_pattern: Str" help="[default: '(?u)\\b\\w\\w+\\b']"> |
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101 <sanitizer> |
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102 <valid initial="string.printable"/> |
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103 </sanitizer> |
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104 </param> |
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105 <param name="feat_ext__tokenizer" type="text" value="null" label="feat_ext__tokenizer: Str" help="[default: 'null']"> |
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106 <sanitizer> |
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107 <valid initial="string.printable"/> |
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108 </sanitizer> |
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109 </param> |
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110 <param name="verbose" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="verbose: Bool" help="[default: No]"/> |
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111 </section> |
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112 </inputs> |
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113 <outputs> |
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114 <data name="classifier" format="qza" label="${tool.name} on ${on_string}: classifier.qza" from_work_dir="classifier.qza"/> |
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115 </outputs> |
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116 <tests/> |
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117 <help> |
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118 QIIME 2: feature-classifier fit-classifier-naive-bayes |
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119 ====================================================== |
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120 Train the naive_bayes classifier |
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121 |
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122 |
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123 Outputs: |
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124 -------- |
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125 :classifier.qza: <no description> |
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126 |
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127 | |
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128 |
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129 Description: |
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130 ------------ |
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131 Create a scikit-learn naive_bayes classifier for reads |
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132 |
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133 |
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134 | |
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135 |
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136 </help> |
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137 <citations> |
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138 <citation type="bibtex">@article{cite1, |
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139 author = {Pedregosa, Fabian and Varoquaux, Gaël and Gramfort, Alexandre and Michel, Vincent and Thirion, Bertrand and Grisel, Olivier and Blondel, Mathieu and Prettenhofer, Peter and Weiss, Ron and Dubourg, Vincent and Vanderplas, Jake and Passos, Alexandre and Cournapeau, David and Brucher, Matthieu and Perrot, Matthieu and Duchesnay, Édouard}, |
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140 journal = {Journal of machine learning research}, |
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141 number = {Oct}, |
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142 pages = {2825--2830}, |
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143 title = {Scikit-learn: Machine learning in Python}, |
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144 volume = {12}, |
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145 year = {2011} |
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146 } |
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147 </citation> |
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148 <citation type="doi">10.1186/s40168-018-0470-z</citation> |
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149 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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150 </citations> |
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151 </tool> |