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comparison qiime2__feature_table__rename_ids.xml @ 0:5e6afe86c5b8 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 19:59:34 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
2 <!--
3 Copyright (c) 2022, QIIME 2 development team.
4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 -->
7 <!--
8 This tool was automatically generated by:
9 q2galaxy (version: 2022.8.1)
10 for:
11 qiime2 (version: 2022.8.1)
12 -->
13 <tool name="qiime2 feature-table rename-ids" id="qiime2__feature_table__rename_ids" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Renames sample or feature ids in a table</description>
15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container>
17 </requirements>
18 <version_command>q2galaxy version feature_table</version_command>
19 <command detect_errors="aggressive">q2galaxy run feature_table rename_ids '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]" help="[required] The table to be renamed">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureTable[Composition]"/>
27 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
28 <filter type="add_value" value="FeatureTable[Frequency]"/>
29 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
30 </options>
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>
32 </param>
33 <conditional name="metadata">
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.">
35 <option value="tsv" selected="true">Metadata from TSV</option>
36 <option value="qza">Metadata from Artifact</option>
37 </param>
38 <when value="tsv">
39 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
40 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
41 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
42 </param>
43 </when>
44 <when value="qza">
45 <param name="source" type="data" format="qza" label="Metadata Source"/>
46 <param name="column" type="text" label="Column Name">
47 <validator type="empty_field"/>
48 </param>
49 </when>
50 </conditional>
51 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
52 <param name="axis" type="select" label="axis: Str % Choices('feature', 'sample')" display="radio">
53 <option value="feature">feature</option>
54 <option value="sample" selected="true">sample</option>
55 </param>
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."/>
57 </section>
58 </inputs>
59 <outputs>
60 <data name="renamed_table" format="qza" label="${tool.name} on ${on_string}: renamed_table.qza" from_work_dir="renamed_table.qza"/>
61 </outputs>
62 <tests/>
63 <help>
64 QIIME 2: feature-table rename-ids
65 =================================
66 Renames sample or feature ids in a table
67
68
69 Outputs:
70 --------
71 :renamed_table.qza: A table which has new ids, where the ids are replaced by values in the `metadata` column.
72
73 |
74
75 Description:
76 ------------
77 Renames the sample or feature ids in a feature table using metadata to define the new ids.
78
79
80 |
81
82 </help>
83 <citations>
84 <citation type="doi">10.1038/s41587-019-0209-9</citation>
85 </citations>
86 </tool>