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comparison qiime2__feature_table__split.xml @ 0:2d32c53669d7 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 21:12:19 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
2 <!--
3 Copyright (c) 2024, 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: 2024.2.1)
10 for:
11 qiime2 (version: 2024.2.0)
12 -->
13 <tool name="qiime2 feature-table split" id="qiime2__feature_table__split" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
14 <description>Split one feature table into many</description>
15 <requirements>
16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
17 </requirements>
18 <version_command>q2galaxy version feature_table</version_command>
19 <command detect_errors="exit_code">q2galaxy run feature_table split '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
22 </configfiles>
23 <inputs>
24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]" help="[required] The table to split.">
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 column defining the groups. Each unique value will define a split feature table.">
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="filter_empty_features" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="filter_empty_features: Bool" help="[default: Yes] If true, features which are not present in a split feature table are dropped."/>
53 </section>
54 </inputs>
55 <outputs>
56 <collection name="tables" type="list">
57 <discover_datasets directory="tables" pattern="__name_and_ext__"/>
58 </collection>
59 </outputs>
60 <tests/>
61 <help>
62 QIIME 2: feature-table split
63 ============================
64 Split one feature table into many
65
66
67 Outputs:
68 --------
69 :tables.qza: Directory where feature tables split based on metadata values should be written.
70
71 |
72
73 Description:
74 ------------
75 Splits one feature table into many feature tables, where splits are defined by values in metadata column.
76
77
78 |
79
80 </help>
81 <citations>
82 <citation type="doi">10.1038/s41587-019-0209-9</citation>
83 </citations>
84 </tool>