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comparison qiime2__phylogeny__iqtree_ultrafast_bootstrap.xml @ 2:adccaaf33660 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 65e4952f33eb335528e8553150e9097e5ea8f556
author q2d2
date Thu, 08 Jun 2023 19:50:07 +0000
parents caa6e396efc4
children 7f29e76a07c2
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4 4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 --> 6 -->
7 <!-- 7 <!--
8 This tool was automatically generated by: 8 This tool was automatically generated by:
9 q2galaxy (version: 2022.11.1) 9 q2galaxy (version: 2023.5.0)
10 for: 10 for:
11 qiime2 (version: 2022.11.1) 11 qiime2 (version: 2023.5.1)
12 --> 12 -->
13 <tool name="qiime2 phylogeny iqtree-ultrafast-bootstrap" id="qiime2__phylogeny__iqtree_ultrafast_bootstrap" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 phylogeny iqtree-ultrafast-bootstrap" id="qiime2__phylogeny__iqtree_ultrafast_bootstrap" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
14 <description>Construct a phylogenetic tree with IQ-TREE with bootstrap supports.</description> 14 <description>Construct a phylogenetic tree with IQ-TREE with bootstrap supports.</description>
15 <requirements> 15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.11</container> 16 <container type="docker">quay.io/qiime2/core:2023.5</container>
17 </requirements> 17 </requirements>
18 <version_command>q2galaxy version phylogeny</version_command> 18 <version_command>q2galaxy version phylogeny</version_command>
19 <command detect_errors="exit_code">q2galaxy run phylogeny iqtree_ultrafast_bootstrap '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run phylogeny iqtree_ultrafast_bootstrap '$inputs'</command>
20 <configfiles> 20 <configfiles>
21 <inputs name="inputs" data_style="paths"/> 21 <inputs name="inputs" data_style="paths"/>
343 <param name="n_max_ufboot_iter" type="integer" min="1" optional="true" label="n_max_ufboot_iter: Int % Range(1, None)" help="[optional] Maximum number of iterations. If not set, program defaults will be used. See IQ-TREE manual for details."/> 343 <param name="n_max_ufboot_iter" type="integer" min="1" optional="true" label="n_max_ufboot_iter: Int % Range(1, None)" help="[optional] Maximum number of iterations. If not set, program defaults will be used. See IQ-TREE manual for details."/>
344 <param name="n_ufboot_steps" type="integer" min="1" optional="true" label="n_ufboot_steps: Int % Range(1, None)" help="[optional] Number of iterations for UFBoot stopping rule. If not set, program defaults will be used.See IQ-TREE manual for details."/> 344 <param name="n_ufboot_steps" type="integer" min="1" optional="true" label="n_ufboot_steps: Int % Range(1, None)" help="[optional] Number of iterations for UFBoot stopping rule. If not set, program defaults will be used.See IQ-TREE manual for details."/>
345 <param name="min_cor_ufboot" type="float" min="0.51" max="0.989999" optional="true" label="min_cor_ufboot: Float % Range(0.51, 0.99)" help="[optional] Minimum correlation coefficient. If not set, program defaults will be used.See IQ-TREE manual for details."/> 345 <param name="min_cor_ufboot" type="float" min="0.51" max="0.989999" optional="true" label="min_cor_ufboot: Float % Range(0.51, 0.99)" help="[optional] Minimum correlation coefficient. If not set, program defaults will be used.See IQ-TREE manual for details."/>
346 <param name="ep_break_ufboot" type="float" min="0.01" max="0.989999" optional="true" label="ep_break_ufboot: Float % Range(0.01, 0.99)" help="[optional] Epsilon value to break tie. If not set, program defaults will be used. See IQ-TREE manual for details."/> 346 <param name="ep_break_ufboot" type="float" min="0.01" max="0.989999" optional="true" label="ep_break_ufboot: Float % Range(0.01, 0.99)" help="[optional] Epsilon value to break tie. If not set, program defaults will be used. See IQ-TREE manual for details."/>
347 <param name="allnni" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="allnni: Bool" help="[default: No] Perform more thorough NNI search."/> 347 <param name="allnni" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="allnni: Bool" help="[default: No] Perform more thorough NNI search."/>
348 <param name="alrt" type="integer" min="1000" optional="true" label="alrt: Int % Range(1000, None)" help="[optional] Single branch test method. Number of bootstrap replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is recomended. Can be used with other 'single branch test methods'. Values reported in the order of: alrt, lbp, abayes."/> 348 <param name="alrt" type="integer" min="1000" optional="true" label="alrt: Int % Range(1000, None)" help="[optional] Single branch test method. Number of bootstrap replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is required. Can be used with other 'single branch test methods'. Values reported in the order of: alrt, lbp, abayes."/>
349 <param name="abayes" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="abayes: Bool" help="[default: No] Single branch test method. Performs an approximate Bayes test. Can be used with other 'single branch test methods' and ultrafast bootstrap. Values reported in the order of: alrt, lbp, abayes, ufboot."/> 349 <param name="abayes" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="abayes: Bool" help="[default: No] Single branch test method. Performs an approximate Bayes test. Can be used with other 'single branch test methods' and ultrafast bootstrap. Values reported in the order of: alrt, lbp, abayes, ufboot."/>
350 <param name="lbp" type="integer" min="1000" optional="true" label="lbp: Int % Range(1000, None)" help="[optional] Single branch test method. Number of bootstrap replicates to perform a fast local bootstrap probability method. Minimum of 1000 replicates is recomended. Can be used with other 'single branch test methods'. Values reported in the order of: alrt, lbp, abayes, ufboot."/> 350 <param name="lbp" type="integer" min="1000" optional="true" label="lbp: Int % Range(1000, None)" help="[optional] Single branch test method. Number of bootstrap replicates to perform a fast local bootstrap probability method. Minimum of 1000 replicates is required. Can be used with other 'single branch test methods'. Values reported in the order of: alrt, lbp, abayes, ufboot."/>
351 <param name="bnni" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="bnni: Bool" help="[default: No] Optimize UFBoot trees by NNI on bootstrap alignment. This option reduces the risk of overestimating branch supports with UFBoot due to severe model violations."/> 351 <param name="bnni" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="bnni: Bool" help="[default: No] Optimize UFBoot trees by NNI on bootstrap alignment. This option reduces the risk of overestimating branch supports with UFBoot due to severe model violations."/>
352 <param name="safe" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="safe: Bool" help="[default: No] Safe likelihood kernel to avoid numerical underflow."/> 352 <param name="safe" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="safe: Bool" help="[default: No] Safe likelihood kernel to avoid numerical underflow."/>
353 </section> 353 </section>
354 </inputs> 354 </inputs>
355 <outputs> 355 <outputs>