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comparison qiime2__alignment__mafft_add.xml @ 3:26215ab0ef72 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author q2d2
date Thu, 25 Apr 2024 20:52:32 +0000
parents 442d1a046fa6
children 51e7e9d2c302
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2:442d1a046fa6 3:26215ab0ef72
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <!-- 2 <!--
3 Copyright (c) 2023, QIIME 2 development team. 3 Copyright (c) 2024, QIIME 2 development team.
4 4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 --> 6 -->
7 <!-- 7 <!--
8 This tool was automatically generated by: 8 This tool was automatically generated by:
9 q2galaxy (version: 2023.5.0) 9 q2galaxy (version: 2024.2.1)
10 for: 10 for:
11 qiime2 (version: 2023.5.1) 11 qiime2 (version: 2024.2.0)
12 --> 12 -->
13 <tool name="qiime2 alignment mafft-add" id="qiime2__alignment__mafft_add" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 alignment mafft-add" id="qiime2__alignment__mafft_add" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
14 <description>Add sequences to multiple sequence alignment with MAFFT.</description> 14 <description>Add sequences to multiple sequence alignment with MAFFT.</description>
15 <requirements> 15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2023.5</container> 16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
17 </requirements> 17 </requirements>
18 <version_command>q2galaxy version alignment</version_command> 18 <version_command>q2galaxy version alignment</version_command>
19 <command detect_errors="exit_code">q2galaxy run alignment mafft_add '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run alignment mafft_add '$inputs'</command>
20 <configfiles> 20 <configfiles>
21 <inputs name="inputs" data_style="paths"/> 21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
22 </configfiles> 22 </configfiles>
23 <inputs> 23 <inputs>
24 <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required] The alignment to which sequences should be added."> 24 <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required] The alignment to which sequences should be added.">
25 <options options_filter_attribute="metadata.semantic_type"> 25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureData[AlignedSequence]"/> 26 <filter type="add_value" value="FeatureData[AlignedSequence]"/>
32 <filter type="add_value" value="FeatureData[Sequence]"/> 32 <filter type="add_value" value="FeatureData[Sequence]"/>
33 </options> 33 </options>
34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator> 34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
35 </param> 35 </param>
36 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> 36 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
37 <conditional name="__q2galaxy__GUI__conditional__n_threads__">
38 <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)">
39 <option value="auto">auto (Str)</option>
40 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
41 </param>
42 <when value="auto">
43 <param name="n_threads" type="hidden" value="auto"/>
44 </when>
45 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
46 <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)"/>
47 </when>
48 </conditional>
49 <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"/> 37 <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"/>
50 <param name="addfragments" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="addfragments: Bool" help="[default: No] Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used."/> 38 <param name="addfragments" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="addfragments: Bool" help="[default: No] Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used."/>
51 </section> 39 </section>
52 </inputs> 40 </inputs>
53 <outputs> 41 <outputs>