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comparison qiime2__alignment__mafft.xml @ 0:f393282d35ee draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 19:18:07 +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 alignment mafft" id="qiime2__alignment__mafft" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>De novo multiple sequence alignment with MAFFT</description>
15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container>
17 </requirements>
18 <version_command>q2galaxy version alignment</version_command>
19 <command detect_errors="aggressive">q2galaxy run alignment mafft '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
24 <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required] The sequences to be aligned.">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureData[Sequence]"/>
27 </options>
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
29 </param>
30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
31 <conditional name="__q2galaxy__GUI__conditional__n_threads__">
32 <param name="__q2galaxy__GUI__select__" type="select" label="n_threads: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1] The number of threads. (Use `auto` to automatically use all available cores)">
33 <option value="auto">auto (Str)</option>
34 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
35 </param>
36 <when value="auto">
37 <param name="n_threads" type="hidden" value="auto"/>
38 </when>
39 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
40 <param name="n_threads" type="integer" min="1" value="1" label="n_threads: Int % Range(1, None)" help="[default: 1] The number of threads. (Use `auto` to automatically use all available cores)"/>
41 </when>
42 </conditional>
43 <param name="parttree" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="parttree: Bool" help="[default: No] This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default"/>
44 </section>
45 </inputs>
46 <outputs>
47 <data name="alignment" format="qza" label="${tool.name} on ${on_string}: alignment.qza" from_work_dir="alignment.qza"/>
48 </outputs>
49 <tests/>
50 <help>
51 QIIME 2: alignment mafft
52 ========================
53 De novo multiple sequence alignment with MAFFT
54
55
56 Outputs:
57 --------
58 :alignment.qza: The aligned sequences.
59
60 |
61
62 Description:
63 ------------
64 Perform de novo multiple sequence alignment using MAFFT.
65
66
67 |
68
69 </help>
70 <citations>
71 <citation type="doi">10.1093/molbev/mst010</citation>
72 <citation type="doi">10.1038/s41587-019-0209-9</citation>
73 </citations>
74 </tool>