comparison qiime2__phylogeny__robinson_foulds.xml @ 0:c27ffaac5054 draft

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author q2d2
date Mon, 29 Aug 2022 20:19:13 +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 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 '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
24 <param name="trees" type="data" format="qza" label="trees: List[Phylogeny[Rooted | Unrooted]]" help="[required] Phylogenetic trees to compare with Robinson-Foulds. Rooting information and branch lengths are ignored by this metric." multiple="true">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="Phylogeny[Unrooted]"/>
27 <filter type="add_value" value="Phylogeny[Rooted]"/>
28 </options>
29 </param>
30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
31 <repeat name="labels" help="[optional] Labels to use for the tree names in the distance matrix. If ommited, labels will be &quot;tree_n&quot; where &quot;n&quot; ranges from 1..N. The number of labels must match the number of trees." title="labels: List[Str]">
32 <param name="element" type="text" label="element: Str" help="[required]">
33 <sanitizer>
34 <valid initial="string.printable"/>
35 </sanitizer>
36 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
37 </param>
38 </repeat>
39 <param name="missing_tips" type="select" label="missing_tips: Str % Choices('error', 'intersect-all')" display="radio">
40 <option value="error" selected="true">error</option>
41 <option value="intersect-all">intersect-all</option>
42 </param>
43 </section>
44 </inputs>
45 <outputs>
46 <data name="distance_matrix" format="qza" label="${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>