Mercurial > repos > q2d2 > qiime2__sample_classifier__classify_samples_from_dist
annotate qiime2__sample_classifier__classify_samples_from_dist.xml @ 4:2dad5e35f34c draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit c7e80dcda727ce63b42aa8a946e9330310929797
author | q2d2 |
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date | Mon, 03 Jun 2024 23:31:43 +0000 |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_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__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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2 <!-- |
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3287c7a4f1a6
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3 Copyright (c) 2024, QIIME 2 development team. |
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4 |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_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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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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6 --> |
e3547924b96d
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_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__sample_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__sample_classifier commit c7e80dcda727ce63b42aa8a946e9330310929797
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9 q2galaxy (version: 2024.5.0) |
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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__sample_classifier commit c7e80dcda727ce63b42aa8a946e9330310929797
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11 qiime2 (version: 2024.5.0) |
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12 --> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit c7e80dcda727ce63b42aa8a946e9330310929797
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13 <tool name="qiime2 sample-classifier classify-samples-from-dist" id="qiime2__sample_classifier__classify_samples_from_dist" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause"> |
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14 <description>Run k-nearest-neighbors on a labeled distance matrix.</description> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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15 <requirements> |
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16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container> |
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17 </requirements> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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18 <version_command>q2galaxy version sample_classifier</version_command> |
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19 <command detect_errors="exit_code">q2galaxy run sample_classifier classify_samples_from_dist '$inputs'</command> |
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20 <configfiles> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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21 <inputs name="inputs" data_style="staging_path_and_source_path"/> |
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22 </configfiles> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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23 <inputs> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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24 <param name="distance_matrix" type="data" format="qza" label="distance_matrix: DistanceMatrix" help="[required] a distance matrix"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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26 <filter type="add_value" value="DistanceMatrix"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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 ['DistanceMatrix']</validator> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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29 </param> |
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30 <conditional name="metadata"> |
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31 <param name="type" type="select" label="metadata: MetadataColumn[Categorical]" help="[required] Categorical metadata column to use as prediction target."> |
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32 <option value="tsv" selected="true">Metadata from TSV</option> |
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33 <option value="qza">Metadata from Artifact</option> |
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34 </param> |
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35 <when value="tsv"> |
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36 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> |
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37 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true"> |
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38 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator> |
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39 </param> |
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40 </when> |
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41 <when value="qza"> |
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42 <param name="source" type="data" format="qza" label="Metadata Source"/> |
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43 <param name="column" type="text" label="Column Name"> |
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44 <validator type="empty_field"/> |
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45 </param> |
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46 </when> |
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47 </conditional> |
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48 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> |
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49 <param name="k" type="integer" value="1" label="k: Int" help="[default: 1] Number of nearest neighbors"/> |
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50 <param name="cv" type="integer" min="1" value="5" label="cv: Int % Range(1, None)" help="[default: 5] Number of k-fold cross-validations to perform."/> |
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51 <param name="random_state" type="integer" optional="true" label="random_state: Int" help="[optional] Seed used by random number generator."/> |
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52 <param name="palette" type="select" label="palette: Str % Choices('YellowOrangeBrown', 'YellowOrangeRed', 'OrangeRed', 'PurpleRed', 'RedPurple', 'BluePurple', 'GreenBlue', 'PurpleBlue', 'YellowGreen', 'summer', 'copper', 'viridis', 'cividis', 'plasma', 'inferno', 'magma', 'sirocco', 'drifting', 'melancholy', 'enigma', 'eros', 'spectre', 'ambition', 'mysteriousstains', 'daydream', 'solano', 'navarro', 'dandelions', 'deepblue', 'verve', 'greyscale')"> |
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53 <option value="YellowOrangeBrown">YellowOrangeBrown</option> |
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54 <option value="YellowOrangeRed">YellowOrangeRed</option> |
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55 <option value="OrangeRed">OrangeRed</option> |
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56 <option value="PurpleRed">PurpleRed</option> |
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57 <option value="RedPurple">RedPurple</option> |
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58 <option value="BluePurple">BluePurple</option> |
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59 <option value="GreenBlue">GreenBlue</option> |
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60 <option value="PurpleBlue">PurpleBlue</option> |
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61 <option value="YellowGreen">YellowGreen</option> |
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62 <option value="summer">summer</option> |
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63 <option value="copper">copper</option> |
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64 <option value="viridis">viridis</option> |
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65 <option value="cividis">cividis</option> |
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66 <option value="plasma">plasma</option> |
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67 <option value="inferno">inferno</option> |
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68 <option value="magma">magma</option> |
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69 <option value="sirocco" selected="true">sirocco</option> |
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70 <option value="drifting">drifting</option> |
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71 <option value="melancholy">melancholy</option> |
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72 <option value="enigma">enigma</option> |
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73 <option value="eros">eros</option> |
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74 <option value="spectre">spectre</option> |
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75 <option value="ambition">ambition</option> |
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76 <option value="mysteriousstains">mysteriousstains</option> |
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77 <option value="daydream">daydream</option> |
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78 <option value="solano">solano</option> |
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79 <option value="navarro">navarro</option> |
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80 <option value="dandelions">dandelions</option> |
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81 <option value="deepblue">deepblue</option> |
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82 <option value="verve">verve</option> |
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83 <option value="greyscale">greyscale</option> |
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84 </param> |
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85 </section> |
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86 </inputs> |
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87 <outputs> |
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88 <data name="predictions" format="qza" label="${tool.name} on ${on_string}: predictions.qza" from_work_dir="predictions.qza"/> |
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89 <data name="accuracy_results" format="qzv" label="${tool.name} on ${on_string}: accuracy_results.qzv" from_work_dir="accuracy_results.qzv"/> |
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90 </outputs> |
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91 <tests/> |
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92 <help> |
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93 QIIME 2: sample-classifier classify-samples-from-dist |
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94 ===================================================== |
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95 Run k-nearest-neighbors on a labeled distance matrix. |
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96 |
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97 |
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98 Outputs: |
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99 -------- |
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100 :predictions.qza: leave one out predictions for each sample |
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101 :accuracy_results.qzv: Accuracy results visualization. |
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102 |
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103 | |
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104 |
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105 Description: |
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106 ------------ |
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107 Run k-nearest-neighbors on a labeled distance matrix. Return cross-validated (leave one out) predictions and accuracy. k = 1 by default |
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108 |
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109 |
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110 | |
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111 |
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112 </help> |
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113 <citations> |
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114 <citation type="doi">10.21105/joss.00934</citation> |
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115 <citation type="bibtex">@article{cite2, |
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116 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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117 journal = {Journal of machine learning research}, |
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118 number = {Oct}, |
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119 pages = {2825--2830}, |
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120 title = {Scikit-learn: Machine learning in Python}, |
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121 volume = {12}, |
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122 year = {2011} |
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123 } |
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124 </citation> |
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125 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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126 </citations> |
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127 </tool> |