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comparison qiime2__feature_table__group.xml @ 0:834bb534ba6d 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 19:54:40 +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 group" id="qiime2__feature_table__group" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Group samples or features by a metadata column</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 group '$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[Frequency]" help="[required] The table to group samples or features on.">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureTable[Frequency]"/>
27 </options>
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
29 </param>
30 <param name="axis" type="select" label="axis: Str % Choices('feature', 'sample')" display="radio">
31 <option value="__q2galaxy__::literal::None">Selection required</option>
32 <option value="feature">feature</option>
33 <option value="sample">sample</option>
34 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
35 </param>
36 <conditional name="metadata">
37 <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`.">
38 <option value="tsv" selected="true">Metadata from TSV</option>
39 <option value="qza">Metadata from Artifact</option>
40 </param>
41 <when value="tsv">
42 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
43 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
44 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
45 </param>
46 </when>
47 <when value="qza">
48 <param name="source" type="data" format="qza" label="Metadata Source"/>
49 <param name="column" type="text" label="Column Name">
50 <validator type="empty_field"/>
51 </param>
52 </when>
53 </conditional>
54 <param name="mode" type="select" label="mode: Str % Choices('mean-ceiling', 'median-ceiling', 'sum')" display="radio">
55 <option value="__q2galaxy__::literal::None">Selection required</option>
56 <option value="mean-ceiling">mean-ceiling</option>
57 <option value="median-ceiling">median-ceiling</option>
58 <option value="sum">sum</option>
59 <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
60 </param>
61 </inputs>
62 <outputs>
63 <data name="grouped_table" format="qza" label="${tool.name} on ${on_string}: grouped_table.qza" from_work_dir="grouped_table.qza"/>
64 </outputs>
65 <tests/>
66 <help>
67 QIIME 2: feature-table group
68 ============================
69 Group samples or features by a metadata column
70
71
72 Outputs:
73 --------
74 :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.
75
76 |
77
78 Description:
79 ------------
80 Group samples or features in a feature table using metadata to define the mapping of IDs to a group.
81
82
83 |
84
85 </help>
86 <citations>
87 <citation type="doi">10.1038/s41587-019-0209-9</citation>
88 </citations>
89 </tool>