Mercurial > repos > q2d2 > qiime2__alignment__mafft_add

comparison qiime2__alignment__mafft_add.xml @ 0:631f37aab464 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 19:18:45 +0000
parents
children 4fde174f0118
comparison
equal deleted inserted replaced
-1:000000000000 0:631f37aab464
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-add" id="qiime2__alignment__mafft_add" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Add sequences to 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_add '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
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">
26 <filter type="add_value" value="FeatureData[AlignedSequence]"/>
27 </options>
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]']</validator>
29 </param>
30 <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required] The sequences to be added.">
31 <options options_filter_attribute="metadata.semantic_type">
32 <filter type="add_value" value="FeatureData[Sequence]"/>
33 </options>
34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
35 </param>
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"/>
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."/>
51 </section>
52 </inputs>
53 <outputs>
54 <data name="expanded_alignment" format="qza" label="${tool.name} on ${on_string}: expanded_alignment.qza" from_work_dir="expanded_alignment.qza"/>
55 </outputs>
56 <tests/>
57 <help>
58 QIIME 2: alignment mafft-add
59 ============================
60 Add sequences to multiple sequence alignment with MAFFT.
61
62
63 Outputs:
64 --------
65 :expanded_alignment.qza: Alignment containing the provided aligned and unaligned sequences.
66
67 |
68
69 Description:
70 ------------
71 Add new sequences to an existing alignment with MAFFT.
72
73
74 |
75
76 </help>
77 <citations>
78 <citation type="doi">10.1093/molbev/mst010</citation>
79 <citation type="doi">10.1038/s41587-019-0209-9</citation>
80 </citations>
81 </tool>