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comparison qiime2__phylogeny__fasttree.xml @ 0:c9eafd561cc4 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 20:16:28 +0000
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-1:000000000000 0:c9eafd561cc4
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 phylogeny fasttree" id="qiime2__phylogeny__fasttree" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Construct a phylogenetic tree with FastTree.</description>
15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container>
17 </requirements>
18 <version_command>q2galaxy version phylogeny</version_command>
19 <command detect_errors="aggressive">q2galaxy run phylogeny fasttree '$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] Aligned sequences to be used for phylogenetic reconstruction.">
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 <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. Using more than one thread runs the non-deterministic variant of `FastTree` (`FastTreeMP`), and may result in a different tree than single-threading. See http://www.microbesonline.org/fasttree/#OpenMP for details. (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. Using more than one thread runs the non-deterministic variant of `FastTree` (`FastTreeMP`), and may result in a different tree than single-threading. See http://www.microbesonline.org/fasttree/#OpenMP for details. (Use `auto` to automatically use all available cores)"/>
41 </when>
42 </conditional>
43 </section>
44 </inputs>
45 <outputs>
46 <data name="tree" format="qza" label="${tool.name} on ${on_string}: tree.qza" from_work_dir="tree.qza"/>
47 </outputs>
48 <tests/>
49 <help>
50 QIIME 2: phylogeny fasttree
51 ===========================
52 Construct a phylogenetic tree with FastTree.
53
54
55 Outputs:
56 --------
57 :tree.qza: The resulting phylogenetic tree.
58
59 |
60
61 Description:
62 ------------
63 Construct a phylogenetic tree with FastTree.
64
65
66 |
67
68 </help>
69 <citations>
70 <citation type="doi">10.1371/journal.pone.0009490</citation>
71 <citation type="doi">10.1038/s41587-019-0209-9</citation>
72 </citations>
73 </tool>