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comparison qiime2__phylogeny__robinson_foulds.xml @ 0:c27ffaac5054 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author | q2d2 |
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date | Mon, 29 Aug 2022 20:19:13 +0000 |
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children | abe6db32295f |
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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 phylogeny robinson-foulds" id="qiime2__phylogeny__robinson_foulds" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> | |
14 <description>Calculate Robinson-Foulds distance between phylogenetic trees.</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 robinson_foulds '$inputs'</command> | |
20 <configfiles> | |
21 <inputs name="inputs" data_style="paths"/> | |
22 </configfiles> | |
23 <inputs> | |
24 <param name="trees" type="data" format="qza" label="trees: List[Phylogeny[Rooted | Unrooted]]" help="[required] Phylogenetic trees to compare with Robinson-Foulds. Rooting information and branch lengths are ignored by this metric." multiple="true"> | |
25 <options options_filter_attribute="metadata.semantic_type"> | |
26 <filter type="add_value" value="Phylogeny[Unrooted]"/> | |
27 <filter type="add_value" value="Phylogeny[Rooted]"/> | |
28 </options> | |
29 </param> | |
30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> | |
31 <repeat name="labels" help="[optional] Labels to use for the tree names in the distance matrix. If ommited, labels will be "tree_n" where "n" ranges from 1..N. The number of labels must match the number of trees." title="labels: List[Str]"> | |
32 <param name="element" type="text" label="element: Str" help="[required]"> | |
33 <sanitizer> | |
34 <valid initial="string.printable"/> | |
35 </sanitizer> | |
36 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> | |
37 </param> | |
38 </repeat> | |
39 <param name="missing_tips" type="select" label="missing_tips: Str % Choices('error', 'intersect-all')" display="radio"> | |
40 <option value="error" selected="true">error</option> | |
41 <option value="intersect-all">intersect-all</option> | |
42 </param> | |
43 </section> | |
44 </inputs> | |
45 <outputs> | |
46 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/> | |
47 </outputs> | |
48 <tests/> | |
49 <help> | |
50 QIIME 2: phylogeny robinson-foulds | |
51 ================================== | |
52 Calculate Robinson-Foulds distance between phylogenetic trees. | |
53 | |
54 | |
55 Outputs: | |
56 -------- | |
57 :distance_matrix.qza: The distances between trees as a symmetric matrix. | |
58 | |
59 | | |
60 | |
61 Description: | |
62 ------------ | |
63 Calculate the Robinson-Foulds symmetric difference metric between two or more phylogenetic trees. | |
64 | |
65 | |
66 | | |
67 | |
68 </help> | |
69 <citations> | |
70 <citation type="bibtex">@article{cite1, | |
71 author = {Robinson, David F and Foulds, Leslie R}, | |
72 journal = {Mathematical biosciences}, | |
73 number = {1-2}, | |
74 pages = {131--147}, | |
75 publisher = {Elsevier}, | |
76 title = {Comparison of phylogenetic trees}, | |
77 volume = {53}, | |
78 year = {1981} | |
79 } | |
80 </citation> | |
81 <citation type="doi">10.1038/s41587-019-0209-9</citation> | |
82 </citations> | |
83 </tool> |