Mercurial > repos > q2d2 > qiime2__feature_table__group
annotate qiime2__feature_table__group.xml @ 5:4acd06f54adc draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 5f71b597c9495eae67a447744fded834f56ca1f7
author | q2d2 |
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date | Wed, 30 Oct 2024 19:51:49 +0000 |
parents | d8d9cde18805 |
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834bb534ba6d
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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1 <?xml version='1.0' encoding='utf-8'?> |
834bb534ba6d
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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2 <!-- |
3
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3 Copyright (c) 2024, QIIME 2 development team. |
0
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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4 |
834bb534ba6d
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) |
834bb534ba6d
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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6 --> |
834bb534ba6d
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 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_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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8 This tool was automatically generated by: |
5
4acd06f54adc
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 5f71b597c9495eae67a447744fded834f56ca1f7
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9 q2galaxy (version: 2024.10.0) |
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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__feature_table commit 5f71b597c9495eae67a447744fded834f56ca1f7
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11 qiime2 (version: 2024.10.1) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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12 --> |
5
4acd06f54adc
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 5f71b597c9495eae67a447744fded834f56ca1f7
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13 <tool name="qiime2 feature-table group" id="qiime2__feature_table__group" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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14 <description>Group samples or features by a metadata column</description> |
5
4acd06f54adc
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 5f71b597c9495eae67a447744fded834f56ca1f7
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15 <xrefs> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 5f71b597c9495eae67a447744fded834f56ca1f7
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16 <xref type="bio.tools">qiime2</xref> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 5f71b597c9495eae67a447744fded834f56ca1f7
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17 </xrefs> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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18 <requirements> |
5
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 5f71b597c9495eae67a447744fded834f56ca1f7
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19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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20 </requirements> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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21 <version_command>q2galaxy version feature_table</version_command> |
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22 <command detect_errors="exit_code">q2galaxy run feature_table group '$inputs'</command> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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23 <configfiles> |
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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25 </configfiles> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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26 <inputs> |
834bb534ba6d
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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27 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] The table to group samples or features on."> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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28 <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_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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29 <filter type="add_value" value="FeatureTable[Frequency]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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30 </options> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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32 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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33 <param name="axis" type="select" label="axis: Str % Choices('feature', 'sample')" display="radio"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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34 <option value="__q2galaxy__::literal::None">Selection required</option> |
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35 <option value="feature">feature</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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36 <option value="sample">sample</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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37 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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38 </param> |
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39 <conditional name="metadata"> |
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40 <param name="type" type="select" label="metadata: MetadataColumn[Categorical]" help="[required] A column defining the groups. Each unique value will become a new ID for the table on the given `axis`."> |
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41 <option value="tsv" selected="true">Metadata from TSV</option> |
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42 <option value="qza">Metadata from Artifact</option> |
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43 </param> |
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44 <when value="tsv"> |
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45 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> |
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46 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true"> |
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47 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator> |
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48 </param> |
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49 </when> |
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50 <when value="qza"> |
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51 <param name="source" type="data" format="qza" label="Metadata Source"/> |
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52 <param name="column" type="text" label="Column Name"> |
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53 <validator type="empty_field"/> |
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54 </param> |
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55 </when> |
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56 </conditional> |
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57 <param name="mode" type="select" label="mode: Str % Choices('mean-ceiling', 'median-ceiling', 'sum')" display="radio"> |
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58 <option value="__q2galaxy__::literal::None">Selection required</option> |
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59 <option value="mean-ceiling">mean-ceiling</option> |
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60 <option value="median-ceiling">median-ceiling</option> |
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61 <option value="sum">sum</option> |
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62 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> |
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63 </param> |
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64 </inputs> |
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65 <outputs> |
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66 <data name="grouped_table" format="qza" label="${tool.name} on ${on_string}: grouped_table.qza" from_work_dir="grouped_table.qza"/> |
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67 </outputs> |
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68 <tests> |
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69 <test> |
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70 <param name="table" value="group.test0.feature-table.qza" ftype="qza"/> |
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71 <param name="axis" value="sample"/> |
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72 <conditional name="metadata"> |
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73 <param name="type" value="tsv"/> |
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74 <param name="source" value="group.test0.sample-metadata.tsv" ftype="qiime2.tabular"/> |
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75 <param name="column" value="3"/> |
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76 </conditional> |
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77 <param name="mode" value="median-ceiling"/> |
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78 <output name="grouped_table" ftype="qza"> |
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79 <assert_contents> |
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80 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> |
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81 <has_line_matching expression="type: FeatureTable\[Frequency\]"/> |
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82 </has_archive_member> |
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83 </assert_contents> |
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84 </output> |
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85 </test> |
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86 </tests> |
0
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87 <help> |
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88 QIIME 2: feature-table group |
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89 ============================ |
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90 Group samples or features by a metadata column |
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91 |
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92 |
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93 Outputs: |
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94 -------- |
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95 :grouped_table.qza: A table that has been grouped along the given `axis`. IDs on that axis are replaced by values in the `metadata` column. |
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96 |
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97 | |
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98 |
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99 Description: |
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100 ------------ |
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101 Group samples or features in a feature table using metadata to define the mapping of IDs to a group. |
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102 |
1
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103 Examples: |
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104 --------- |
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105 |
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106 group_samples |
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107 ************* |
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108 | Combine samples from the same body-site into single sample. Feature frequencies will be the median across the samples being combined, rounded up to the nearest whole number. |
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109 Using the ``qiime2 feature-table group`` tool: |
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110 #. Set *"table"* to ``#: feature-table.qza`` |
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111 #. Set *"axis"* to ``sample`` |
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112 #. For *"metadata"*: |
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113 |
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114 #. Leave as ``Metadata from TSV`` |
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115 #. Set *"Metadata Source"* to ``sample-metadata.tsv`` |
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116 #. Set *"Column Name"* to ``body-site`` |
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117 |
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118 #. Set *"mode"* to ``median-ceiling`` |
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119 #. Press the ``Execute`` button. |
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120 |
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121 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: |
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122 (Renaming is optional, but it will make any subsequent steps easier to complete.) |
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123 |
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124 .. list-table:: |
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125 :align: left |
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126 :header-rows: 1 |
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127 |
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128 * - History Name |
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129 - *"Name"* to set (be sure to press ``Save``) |
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130 * - ``#: qiime2 feature-table group [...] : grouped_table.qza`` |
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131 - ``body-site-table.qza`` |
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132 |
0
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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="doi">10.1038/s41587-019-0209-9</citation> |
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139 </citations> |
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140 </tool> |