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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 20:04:55 +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 gneiss assign-ids" id="qiime2__gneiss__assign_ids" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.</description>
15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container>
17 </requirements>
18 <version_command>q2galaxy version gneiss</version_command>
19 <command detect_errors="aggressive">q2galaxy run gneiss assign_ids '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
24 <param name="input_table" type="data" format="qza" label="input_table: FeatureTable[Frequency]" help="[required] The input table of counts.">
25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureTable[Frequency]"/>
27 </options>
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
29 </param>
30 <param name="input_tree" type="data" format="qza" label="input_tree: Phylogeny[Rooted]" help="[required] The input tree with potential missing ids.">
31 <options options_filter_attribute="metadata.semantic_type">
32 <filter type="add_value" value="Phylogeny[Rooted]"/>
33 </options>
34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator>
35 </param>
36 </inputs>
37 <outputs>
38 <data name="output_table" format="qza" label="${tool.name} on ${on_string}: output_table.qza" from_work_dir="output_table.qza"/>
39 <data name="output_tree" format="qza" label="${tool.name} on ${on_string}: output_tree.qza" from_work_dir="output_tree.qza"/>
40 </outputs>
41 <tests/>
42 <help>
43 QIIME 2: gneiss assign-ids
44 ==========================
45 Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.
46
47
48 Outputs:
49 --------
50 :output_table.qza: A table with features matching the tree tips.
51 :output_tree.qza: A tree with uniquely identifying ids.
52
53 |
54
55 Description:
56 ------------
57 Assigns UUIDs to uniquely identify internal nodes in the tree. Also corrects for polytomies to create strictly bifurcating trees and aligns the table columns with the tree tip names
58
59
60 |
61
62 </help>
63 <citations>
64 <citation type="bibtex">@article{cite1,
65 author = {Morton, James T and Sanders, Jon and Quinn, Robert A and McDonald, Daniel and Gonzalez, Antonio and Vázquez-Baeza, Yoshiki and Navas-Molina, Jose A and Song, Se Jin and Metcalf, Jessica L and Hyde, Embriette R and Lladser, Manuel and Dorrestein, Pieter C and Knight, Rob},
66 journal = {MSystems},
67 number = {1},
68 pages = {e00162--16},
69 publisher = {Am Soc Microbiol},
70 title = {Balance trees reveal microbial niche differentiation},
71 volume = {2},
72 year = {2017}
73 }
74 </citation>
75 <citation type="doi">10.1038/s41587-019-0209-9</citation>
76 </citations>
77 </tool>