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annotate qiime2__feature_table__rename_ids.xml @ 3:b8225d65b620 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author q2d2
date Thu, 25 Apr 2024 21:09:02 +0000
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children f73f0cda6560
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2024, QIIME 2 development team.
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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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7 <!--
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8 This tool was automatically generated by:
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9 q2galaxy (version: 2024.2.1)
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10 for:
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11 qiime2 (version: 2024.2.0)
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12 -->
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13 <tool name="qiime2 feature-table rename-ids" id="qiime2__feature_table__rename_ids" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
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14 <description>Renames sample or feature ids in a table</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
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17 </requirements>
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18 <version_command>q2galaxy version feature_table</version_command>
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19 <command detect_errors="exit_code">q2galaxy run feature_table rename_ids '$inputs'</command>
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20 <configfiles>
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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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23 <inputs>
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24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]" help="[required] The table to be renamed">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureTable[Composition]"/>
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27 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
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28 <filter type="add_value" value="FeatureTable[Frequency]"/>
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29 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
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30 </options>
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31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
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32 </param>
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33 <conditional name="metadata">
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34 <param name="type" type="select" label="metadata: MetadataColumn[Categorical]" help="[required] A metadata column defining the new ids. Each original id must map to a new unique id. If strict mode is used, then every id in the original table must have a new id.">
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35 <option value="tsv" selected="true">Metadata from TSV</option>
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36 <option value="qza">Metadata from Artifact</option>
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37 </param>
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38 <when value="tsv">
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39 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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40 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
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41 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
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42 </param>
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43 </when>
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44 <when value="qza">
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45 <param name="source" type="data" format="qza" label="Metadata Source"/>
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46 <param name="column" type="text" label="Column Name">
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47 <validator type="empty_field"/>
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48 </param>
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49 </when>
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50 </conditional>
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51 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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52 <param name="axis" type="select" label="axis: Str % Choices('feature', 'sample')" display="radio">
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53 <option value="feature">feature</option>
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54 <option value="sample" selected="true">sample</option>
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55 </param>
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56 <param name="strict" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="strict: Bool" help="[default: No] Whether the naming needs to be strict (each id in the table must have a new id). Otherwise, only the ids described in `metadata` will be renamed and the others will keep their original id names."/>
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57 </section>
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58 </inputs>
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59 <outputs>
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60 <data name="renamed_table" format="qza" label="${tool.name} on ${on_string}: renamed_table.qza" from_work_dir="renamed_table.qza"/>
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61 </outputs>
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62 <tests/>
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63 <help>
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64 QIIME 2: feature-table rename-ids
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65 =================================
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66 Renames sample or feature ids in a table
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67
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68
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69 Outputs:
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70 --------
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71 :renamed_table.qza: A table which has new ids, where the ids are replaced by values in the `metadata` column.
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73 |
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75 Description:
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76 ------------
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77 Renames the sample or feature ids in a feature table using metadata to define the new ids.
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78
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79
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80 |
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81
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82 </help>
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83 <citations>
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84 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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85 </citations>
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86 </tool>