comparison qiime2__phylogeny__raxml_rapid_bootstrap.xml @ 0:3bb5efe0ee0c draft

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 20:17:37 +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 raxml-rapid-bootstrap" id="qiime2__phylogeny__raxml_rapid_bootstrap" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Construct a phylogenetic tree with bootstrap supports using RAxML.</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 raxml_rapid_bootstrap '$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 <param name="seed" type="integer" optional="true" label="seed: Int" help="[optional] Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen."/>
32 <param name="rapid_bootstrap_seed" type="integer" optional="true" label="rapid_bootstrap_seed: Int" help="[optional] Specify a random seed for rapid bootstrapping. This allows you to reproduce rapid bootstrap results. If not supplied then one will be randomly chosen."/>
33 <param name="bootstrap_replicates" type="integer" min="10" value="100" label="bootstrap_replicates: Int % Range(10, None)" help="[default: 100] The number of bootstrap searches to perform."/>
34 <param name="n_threads" type="integer" min="1" value="1" label="n_threads: Int % Range(1, None)" help="[default: 1] The number of threads to use for multithreaded processing. Using more than one thread will enable the PTHREADS version of RAxML."/>
35 <param name="raxml_version" type="select" label="raxml_version: Str % Choices('Standard', 'SSE3', 'AVX2')" display="radio">
36 <option value="Standard" selected="true">Standard</option>
37 <option value="SSE3">SSE3</option>
38 <option value="AVX2">AVX2</option>
39 </param>
40 <param name="substitution_model" type="select" label="substitution_model: Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI')" display="radio">
41 <option value="GTRGAMMA" selected="true">GTRGAMMA</option>
42 <option value="GTRGAMMAI">GTRGAMMAI</option>
43 <option value="GTRCAT">GTRCAT</option>
44 <option value="GTRCATI">GTRCATI</option>
45 </param>
46 </section>
47 </inputs>
48 <outputs>
49 <data name="tree" format="qza" label="${tool.name} on ${on_string}: tree.qza" from_work_dir="tree.qza"/>
50 </outputs>
51 <tests/>
52 <help>
53 QIIME 2: phylogeny raxml-rapid-bootstrap
54 ========================================
55 Construct a phylogenetic tree with bootstrap supports using RAxML.
56
57
58 Outputs:
59 --------
60 :tree.qza: The resulting phylogenetic tree.
61
62 |
63
64 Description:
65 ------------
66 Construct a phylogenetic tree with RAxML with the addition of rapid bootstrapping support values. See: https://sco.h-its.org/exelixis/web/software/raxml/
67
68
69 |
70
71 </help>
72 <citations>
73 <citation type="doi">10.1093/bioinformatics/btu033</citation>
74 <citation type="doi">10.1080/10635150802429642</citation>
75 <citation type="doi">10.1038/s41587-019-0209-9</citation>
76 </citations>
77 </tool>