Mercurial > repos > q2d2 > qiime2__phylogeny__iqtree_ultrafast_bootstrap
changeset 0:3d179bb09652 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 20:18:48 +0000 |
| parents | |
| children | caa6e396efc4 |
| files | qiime2__phylogeny__iqtree_ultrafast_bootstrap.xml test-data/.gitkeep |
| diffstat | 1 files changed, 386 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__phylogeny__iqtree_ultrafast_bootstrap.xml Mon Aug 29 20:18:48 2022 +0000 @@ -0,0 +1,386 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2022, QIIME 2 development team. + +Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) +--> +<!-- +This tool was automatically generated by: + q2galaxy (version: 2022.8.1) +for: + qiime2 (version: 2022.8.1) +--> +<tool name="qiime2 phylogeny iqtree-ultrafast-bootstrap" id="qiime2__phylogeny__iqtree_ultrafast_bootstrap" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Construct a phylogenetic tree with IQ-TREE with bootstrap supports.</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version phylogeny</version_command> + <command detect_errors="aggressive">q2galaxy run phylogeny iqtree_ultrafast_bootstrap '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required] Aligned sequences to be used for phylogenetic reconstruction."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureData[AlignedSequence]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]']</validator> + </param> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="seed" type="integer" optional="true" label="seed: Int" help="[optional] Random number seed. If not set, program defaults will be used. See IQ-TREE manual for details."/> + <conditional name="__q2galaxy__GUI__conditional__n_cores__"> + <param name="__q2galaxy__GUI__select__" type="select" label="n_cores: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1] The number of cores to use for parallel processing. Use `auto` to let IQ-TREE automatically determine the optimal number of cores to use."> + <option value="auto">auto (Str)</option> + <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option> + </param> + <when value="auto"> + <param name="n_cores" type="hidden" value="auto"/> + </when> + <when value="__q2galaxy__::control::Int X Range(1__comma__ None)"> + <param name="n_cores" type="integer" min="1" value="1" label="n_cores: Int % Range(1, None)" help="[default: 1] The number of cores to use for parallel processing. Use `auto` to let IQ-TREE automatically determine the optimal number of cores to use."/> + </when> + </conditional> + <param name="n_cores_max" type="integer" min="2" optional="true" label="n_cores_max: Int % Range(2, None)" help="[optional] Limits the maximum number of cores to be used when 'n_cores' is set to 'auto'."/> + <param name="n_runs" type="integer" min="1" value="1" label="n_runs: Int % Range(1, None)" help="[default: 1] Number of indepedent runs. Multiple independent runs (e.g. 10) can outperform a single run in terms of likelihood maximisation."/> + <param name="substitution_model" type="select" label="substitution_model: Str % Choices('JC', 'JC+I', 'JC+G', 'JC+I+G', 'JC+R2', 'JC+R3', 'JC+R4', 'JC+R5', 'JC+R6', 'JC+R7', 'JC+R8', 'JC+R9', 'JC+R10', 'F81', 'F81+I', 'F81+G', 'F81+I+G', 'F81+R2', 'F81+R3', 'F81+R4', 'F81+R5', 'F81+R6', 'F81+R7', 'F81+R8', 'F81+R9', 'F81+R10', 'K80', 'K80+I', 'K80+G', 'K80+I+G', 'K80+R2', 'K80+R3', 'K80+R4', 'K80+R5', 'K80+R6', 'K80+R7', 'K80+R8', 'K80+R9', 'K80+R10', 'HKY', 'HKY+I', 'HKY+G', 'HKY+I+G', 'HKY+R2', 'HKY+R3', 'HKY+R4', 'HKY+R5', 'HKY+R6', 'HKY+R7', 'HKY+R8', 'HKY+R9', 'HKY+R10', 'TNe', 'TNe+I', 'TNe+G', 'TNe+I+G', 'TNe+R2', 'TNe+R3', 'TNe+R4', 'TNe+R5', 'TNe+R6', 'TNe+R7', 'TNe+R8', 'TNe+R9', 'TNe+R10', 'TN', 'TN+I', 'TN+G', 'TN+I+G', 'TN+R2', 'TN+R3', 'TN+R4', 'TN+R5', 'TN+R6', 'TN+R7', 'TN+R8', 'TN+R9', 'TN+R10', 'K81', 'K81+I', 'K81+G', 'K81+I+G', 'K81+R2', 'K81+R3', 'K81+R4', 'K81+R5', 'K81+R6', 'K81+R7', 'K81+R8', 'K81+R9', 'K81+R10', 'K81u', 'K81u+I', 'K81u+G', 'K81u+I+G', 'K81u+R2', 'K81u+R3', 'K81u+R4', 'K81u+R5', 'K81u+R6', 'K81u+R7', 'K81u+R8', 'K81u+R9', 'K81u+R10', 'TPM2', 'TPM2+I', 'TPM2+G', 'TPM2+I+G', 'TPM2+R2', 'TPM2+R3', 'TPM2+R4', 'TPM2+R5', 'TPM2+R6', 'TPM2+R7', 'TPM2+R8', 'TPM2+R9', 'TPM2+R10', 'TPM2u', 'TPM2u+I', 'TPM2u+G', 'TPM2u+I+G', 'TPM2u+R2', 'TPM2u+R3', 'TPM2u+R4', 'TPM2u+R5', 'TPM2u+R6', 'TPM2u+R7', 'TPM2u+R8', 'TPM2u+R9', 'TPM2u+R10', 'TPM3', 'TPM3+I', 'TPM3+G', 'TPM3+I+G', 'TPM3+R2', 'TPM3+R3', 'TPM3+R4', 'TPM3+R5', 'TPM3+R6', 'TPM3+R7', 'TPM3+R8', 'TPM3+R9', 'TPM3+R10', 'TPM3u', 'TPM3u+I', 'TPM3u+G', 'TPM3u+I+G', 'TPM3u+R2', 'TPM3u+R3', 'TPM3u+R4', 'TPM3u+R5', 'TPM3u+R6', 'TPM3u+R7', 'TPM3u+R8', 'TPM3u+R9', 'TPM3u+R10', 'TIMe', 'TIMe+I', 'TIMe+G', 'TIMe+I+G', 'TIMe+R2', 'TIMe+R3', 'TIMe+R4', 'TIMe+R5', 'TIMe+R6', 'TIMe+R7', 'TIMe+R8', 'TIMe+R9', 'TIMe+R10', 'TIM', 'TIM+I', 'TIM+G', 'TIM+I+G', 'TIM+R2', 'TIM+R3', 'TIM+R4', 'TIM+R5', 'TIM+R6', 'TIM+R7', 'TIM+R8', 'TIM+R9', 'TIM+R10', 'TIM2e', 'TIM2e+I', 'TIM2e+G', 'TIM2e+I+G', 'TIM2e+R2', 'TIM2e+R3', 'TIM2e+R4', 'TIM2e+R5', 'TIM2e+R6', 'TIM2e+R7', 'TIM2e+R8', 'TIM2e+R9', 'TIM2e+R10', 'TIM2', 'TIM2+I', 'TIM2+G', 'TIM2+I+G', 'TIM2+R2', 'TIM2+R3', 'TIM2+R4', 'TIM2+R5', 'TIM2+R6', 'TIM2+R7', 'TIM2+R8', 'TIM2+R9', 'TIM2+R10', 'TIM3e', 'TIM3e+I', 'TIM3e+G', 'TIM3e+I+G', 'TIM3e+R2', 'TIM3e+R3', 'TIM3e+R4', 'TIM3e+R5', 'TIM3e+R6', 'TIM3e+R7', 'TIM3e+R8', 'TIM3e+R9', 'TIM3e+R10', 'TIM3', 'TIM3+I', 'TIM3+G', 'TIM3+I+G', 'TIM3+R2', 'TIM3+R3', 'TIM3+R4', 'TIM3+R5', 'TIM3+R6', 'TIM3+R7', 'TIM3+R8', 'TIM3+R9', 'TIM3+R10', 'TVMe', 'TVMe+I', 'TVMe+G', 'TVMe+I+G', 'TVMe+R2', 'TVMe+R3', 'TVMe+R4', 'TVMe+R5', 'TVMe+R6', 'TVMe+R7', 'TVMe+R8', 'TVMe+R9', 'TVMe+R10', 'TVM', 'TVM+I', 'TVM+G', 'TVM+I+G', 'TVM+R2', 'TVM+R3', 'TVM+R4', 'TVM+R5', 'TVM+R6', 'TVM+R7', 'TVM+R8', 'TVM+R9', 'TVM+R10', 'SYM', 'SYM+I', 'SYM+G', 'SYM+I+G', 'SYM+R2', 'SYM+R3', 'SYM+R4', 'SYM+R5', 'SYM+R6', 'SYM+R7', 'SYM+R8', 'SYM+R9', 'SYM+R10', 'GTR', 'GTR+I', 'GTR+G', 'GTR+I+G', 'GTR+R2', 'GTR+R3', 'GTR+R4', 'GTR+R5', 'GTR+R6', 'GTR+R7', 'GTR+R8', 'GTR+R9', 'GTR+R10', 'MFP', 'TEST')"> + <option value="JC">JC</option> + <option value="JC+I">JC+I</option> + <option value="JC+G">JC+G</option> + <option value="JC+I+G">JC+I+G</option> + <option value="JC+R2">JC+R2</option> + <option value="JC+R3">JC+R3</option> + <option value="JC+R4">JC+R4</option> + <option value="JC+R5">JC+R5</option> + <option value="JC+R6">JC+R6</option> + <option value="JC+R7">JC+R7</option> + <option value="JC+R8">JC+R8</option> + <option value="JC+R9">JC+R9</option> + <option value="JC+R10">JC+R10</option> + <option value="F81">F81</option> + <option value="F81+I">F81+I</option> + <option value="F81+G">F81+G</option> + <option value="F81+I+G">F81+I+G</option> + <option value="F81+R2">F81+R2</option> + <option value="F81+R3">F81+R3</option> + <option value="F81+R4">F81+R4</option> + <option value="F81+R5">F81+R5</option> + <option value="F81+R6">F81+R6</option> + <option value="F81+R7">F81+R7</option> + <option value="F81+R8">F81+R8</option> + <option value="F81+R9">F81+R9</option> + <option value="F81+R10">F81+R10</option> + <option value="K80">K80</option> + <option value="K80+I">K80+I</option> + <option value="K80+G">K80+G</option> + <option value="K80+I+G">K80+I+G</option> + <option value="K80+R2">K80+R2</option> + <option value="K80+R3">K80+R3</option> + <option value="K80+R4">K80+R4</option> + <option value="K80+R5">K80+R5</option> + <option value="K80+R6">K80+R6</option> + <option value="K80+R7">K80+R7</option> + <option value="K80+R8">K80+R8</option> + <option value="K80+R9">K80+R9</option> + <option value="K80+R10">K80+R10</option> + <option value="HKY">HKY</option> + <option value="HKY+I">HKY+I</option> + <option value="HKY+G">HKY+G</option> + <option value="HKY+I+G">HKY+I+G</option> + <option value="HKY+R2">HKY+R2</option> + <option value="HKY+R3">HKY+R3</option> + <option value="HKY+R4">HKY+R4</option> + <option value="HKY+R5">HKY+R5</option> + <option value="HKY+R6">HKY+R6</option> + <option value="HKY+R7">HKY+R7</option> + <option value="HKY+R8">HKY+R8</option> + <option value="HKY+R9">HKY+R9</option> + <option value="HKY+R10">HKY+R10</option> + <option value="TNe">TNe</option> + <option value="TNe+I">TNe+I</option> + <option value="TNe+G">TNe+G</option> + <option value="TNe+I+G">TNe+I+G</option> + <option value="TNe+R2">TNe+R2</option> + <option value="TNe+R3">TNe+R3</option> + <option value="TNe+R4">TNe+R4</option> + <option value="TNe+R5">TNe+R5</option> + <option value="TNe+R6">TNe+R6</option> + <option value="TNe+R7">TNe+R7</option> + <option value="TNe+R8">TNe+R8</option> + <option value="TNe+R9">TNe+R9</option> + <option value="TNe+R10">TNe+R10</option> + <option value="TN">TN</option> + <option value="TN+I">TN+I</option> + <option value="TN+G">TN+G</option> + <option value="TN+I+G">TN+I+G</option> + <option value="TN+R2">TN+R2</option> + <option value="TN+R3">TN+R3</option> + <option value="TN+R4">TN+R4</option> + <option value="TN+R5">TN+R5</option> + <option value="TN+R6">TN+R6</option> + <option value="TN+R7">TN+R7</option> + <option value="TN+R8">TN+R8</option> + <option value="TN+R9">TN+R9</option> + <option value="TN+R10">TN+R10</option> + <option value="K81">K81</option> + <option value="K81+I">K81+I</option> + <option value="K81+G">K81+G</option> + <option value="K81+I+G">K81+I+G</option> + <option value="K81+R2">K81+R2</option> + <option value="K81+R3">K81+R3</option> + <option value="K81+R4">K81+R4</option> + <option value="K81+R5">K81+R5</option> + <option value="K81+R6">K81+R6</option> + <option value="K81+R7">K81+R7</option> + <option value="K81+R8">K81+R8</option> + <option value="K81+R9">K81+R9</option> + <option value="K81+R10">K81+R10</option> + <option value="K81u">K81u</option> + <option value="K81u+I">K81u+I</option> + <option value="K81u+G">K81u+G</option> + <option value="K81u+I+G">K81u+I+G</option> + <option value="K81u+R2">K81u+R2</option> + <option value="K81u+R3">K81u+R3</option> + <option value="K81u+R4">K81u+R4</option> + <option value="K81u+R5">K81u+R5</option> + <option value="K81u+R6">K81u+R6</option> + <option value="K81u+R7">K81u+R7</option> + <option value="K81u+R8">K81u+R8</option> + <option value="K81u+R9">K81u+R9</option> + <option value="K81u+R10">K81u+R10</option> + <option value="TPM2">TPM2</option> + <option value="TPM2+I">TPM2+I</option> + <option value="TPM2+G">TPM2+G</option> + <option value="TPM2+I+G">TPM2+I+G</option> + <option value="TPM2+R2">TPM2+R2</option> + <option value="TPM2+R3">TPM2+R3</option> + <option value="TPM2+R4">TPM2+R4</option> + <option value="TPM2+R5">TPM2+R5</option> + <option value="TPM2+R6">TPM2+R6</option> + <option value="TPM2+R7">TPM2+R7</option> + <option value="TPM2+R8">TPM2+R8</option> + <option value="TPM2+R9">TPM2+R9</option> + <option value="TPM2+R10">TPM2+R10</option> + <option value="TPM2u">TPM2u</option> + <option value="TPM2u+I">TPM2u+I</option> + <option value="TPM2u+G">TPM2u+G</option> + <option value="TPM2u+I+G">TPM2u+I+G</option> + <option value="TPM2u+R2">TPM2u+R2</option> + <option value="TPM2u+R3">TPM2u+R3</option> + <option value="TPM2u+R4">TPM2u+R4</option> + <option value="TPM2u+R5">TPM2u+R5</option> + <option value="TPM2u+R6">TPM2u+R6</option> + <option value="TPM2u+R7">TPM2u+R7</option> + <option value="TPM2u+R8">TPM2u+R8</option> + <option value="TPM2u+R9">TPM2u+R9</option> + <option value="TPM2u+R10">TPM2u+R10</option> + <option value="TPM3">TPM3</option> + <option value="TPM3+I">TPM3+I</option> + <option value="TPM3+G">TPM3+G</option> + <option value="TPM3+I+G">TPM3+I+G</option> + <option value="TPM3+R2">TPM3+R2</option> + <option value="TPM3+R3">TPM3+R3</option> + <option value="TPM3+R4">TPM3+R4</option> + <option value="TPM3+R5">TPM3+R5</option> + <option value="TPM3+R6">TPM3+R6</option> + <option value="TPM3+R7">TPM3+R7</option> + <option value="TPM3+R8">TPM3+R8</option> + <option value="TPM3+R9">TPM3+R9</option> + <option value="TPM3+R10">TPM3+R10</option> + <option value="TPM3u">TPM3u</option> + <option value="TPM3u+I">TPM3u+I</option> + <option value="TPM3u+G">TPM3u+G</option> + <option value="TPM3u+I+G">TPM3u+I+G</option> + <option value="TPM3u+R2">TPM3u+R2</option> + <option value="TPM3u+R3">TPM3u+R3</option> + <option value="TPM3u+R4">TPM3u+R4</option> + <option value="TPM3u+R5">TPM3u+R5</option> + <option value="TPM3u+R6">TPM3u+R6</option> + <option value="TPM3u+R7">TPM3u+R7</option> + <option value="TPM3u+R8">TPM3u+R8</option> + <option value="TPM3u+R9">TPM3u+R9</option> + <option value="TPM3u+R10">TPM3u+R10</option> + <option value="TIMe">TIMe</option> + <option value="TIMe+I">TIMe+I</option> + <option value="TIMe+G">TIMe+G</option> + <option value="TIMe+I+G">TIMe+I+G</option> + <option value="TIMe+R2">TIMe+R2</option> + <option value="TIMe+R3">TIMe+R3</option> + <option value="TIMe+R4">TIMe+R4</option> + <option value="TIMe+R5">TIMe+R5</option> + <option value="TIMe+R6">TIMe+R6</option> + <option value="TIMe+R7">TIMe+R7</option> + <option value="TIMe+R8">TIMe+R8</option> + <option value="TIMe+R9">TIMe+R9</option> + <option value="TIMe+R10">TIMe+R10</option> + <option value="TIM">TIM</option> + <option value="TIM+I">TIM+I</option> + <option value="TIM+G">TIM+G</option> + <option value="TIM+I+G">TIM+I+G</option> + <option value="TIM+R2">TIM+R2</option> + <option value="TIM+R3">TIM+R3</option> + <option value="TIM+R4">TIM+R4</option> + <option value="TIM+R5">TIM+R5</option> + <option value="TIM+R6">TIM+R6</option> + <option value="TIM+R7">TIM+R7</option> + <option value="TIM+R8">TIM+R8</option> + <option value="TIM+R9">TIM+R9</option> + <option value="TIM+R10">TIM+R10</option> + <option value="TIM2e">TIM2e</option> + <option value="TIM2e+I">TIM2e+I</option> + <option value="TIM2e+G">TIM2e+G</option> + <option value="TIM2e+I+G">TIM2e+I+G</option> + <option value="TIM2e+R2">TIM2e+R2</option> + <option value="TIM2e+R3">TIM2e+R3</option> + <option value="TIM2e+R4">TIM2e+R4</option> + <option value="TIM2e+R5">TIM2e+R5</option> + <option value="TIM2e+R6">TIM2e+R6</option> + <option value="TIM2e+R7">TIM2e+R7</option> + <option value="TIM2e+R8">TIM2e+R8</option> + <option value="TIM2e+R9">TIM2e+R9</option> + <option value="TIM2e+R10">TIM2e+R10</option> + <option value="TIM2">TIM2</option> + <option value="TIM2+I">TIM2+I</option> + <option value="TIM2+G">TIM2+G</option> + <option value="TIM2+I+G">TIM2+I+G</option> + <option value="TIM2+R2">TIM2+R2</option> + <option value="TIM2+R3">TIM2+R3</option> + <option value="TIM2+R4">TIM2+R4</option> + <option value="TIM2+R5">TIM2+R5</option> + <option value="TIM2+R6">TIM2+R6</option> + <option value="TIM2+R7">TIM2+R7</option> + <option value="TIM2+R8">TIM2+R8</option> + <option value="TIM2+R9">TIM2+R9</option> + <option value="TIM2+R10">TIM2+R10</option> + <option value="TIM3e">TIM3e</option> + <option value="TIM3e+I">TIM3e+I</option> + <option value="TIM3e+G">TIM3e+G</option> + <option value="TIM3e+I+G">TIM3e+I+G</option> + <option value="TIM3e+R2">TIM3e+R2</option> + <option value="TIM3e+R3">TIM3e+R3</option> + <option value="TIM3e+R4">TIM3e+R4</option> + <option value="TIM3e+R5">TIM3e+R5</option> + <option value="TIM3e+R6">TIM3e+R6</option> + <option value="TIM3e+R7">TIM3e+R7</option> + <option value="TIM3e+R8">TIM3e+R8</option> + <option value="TIM3e+R9">TIM3e+R9</option> + <option value="TIM3e+R10">TIM3e+R10</option> + <option value="TIM3">TIM3</option> + <option value="TIM3+I">TIM3+I</option> + <option value="TIM3+G">TIM3+G</option> + <option value="TIM3+I+G">TIM3+I+G</option> + <option value="TIM3+R2">TIM3+R2</option> + <option value="TIM3+R3">TIM3+R3</option> + <option value="TIM3+R4">TIM3+R4</option> + <option value="TIM3+R5">TIM3+R5</option> + <option value="TIM3+R6">TIM3+R6</option> + <option value="TIM3+R7">TIM3+R7</option> + <option value="TIM3+R8">TIM3+R8</option> + <option value="TIM3+R9">TIM3+R9</option> + <option value="TIM3+R10">TIM3+R10</option> + <option value="TVMe">TVMe</option> + <option value="TVMe+I">TVMe+I</option> + <option value="TVMe+G">TVMe+G</option> + <option value="TVMe+I+G">TVMe+I+G</option> + <option value="TVMe+R2">TVMe+R2</option> + <option value="TVMe+R3">TVMe+R3</option> + <option value="TVMe+R4">TVMe+R4</option> + <option value="TVMe+R5">TVMe+R5</option> + <option value="TVMe+R6">TVMe+R6</option> + <option value="TVMe+R7">TVMe+R7</option> + <option value="TVMe+R8">TVMe+R8</option> + <option value="TVMe+R9">TVMe+R9</option> + <option value="TVMe+R10">TVMe+R10</option> + <option value="TVM">TVM</option> + <option value="TVM+I">TVM+I</option> + <option value="TVM+G">TVM+G</option> + <option value="TVM+I+G">TVM+I+G</option> + <option value="TVM+R2">TVM+R2</option> + <option value="TVM+R3">TVM+R3</option> + <option value="TVM+R4">TVM+R4</option> + <option value="TVM+R5">TVM+R5</option> + <option value="TVM+R6">TVM+R6</option> + <option value="TVM+R7">TVM+R7</option> + <option value="TVM+R8">TVM+R8</option> + <option value="TVM+R9">TVM+R9</option> + <option value="TVM+R10">TVM+R10</option> + <option value="SYM">SYM</option> + <option value="SYM+I">SYM+I</option> + <option value="SYM+G">SYM+G</option> + <option value="SYM+I+G">SYM+I+G</option> + <option value="SYM+R2">SYM+R2</option> + <option value="SYM+R3">SYM+R3</option> + <option value="SYM+R4">SYM+R4</option> + <option value="SYM+R5">SYM+R5</option> + <option value="SYM+R6">SYM+R6</option> + <option value="SYM+R7">SYM+R7</option> + <option value="SYM+R8">SYM+R8</option> + <option value="SYM+R9">SYM+R9</option> + <option value="SYM+R10">SYM+R10</option> + <option value="GTR">GTR</option> + <option value="GTR+I">GTR+I</option> + <option value="GTR+G">GTR+G</option> + <option value="GTR+I+G">GTR+I+G</option> + <option value="GTR+R2">GTR+R2</option> + <option value="GTR+R3">GTR+R3</option> + <option value="GTR+R4">GTR+R4</option> + <option value="GTR+R5">GTR+R5</option> + <option value="GTR+R6">GTR+R6</option> + <option value="GTR+R7">GTR+R7</option> + <option value="GTR+R8">GTR+R8</option> + <option value="GTR+R9">GTR+R9</option> + <option value="GTR+R10">GTR+R10</option> + <option value="MFP" selected="true">MFP</option> + <option value="TEST">TEST</option> + </param> + <param name="bootstrap_replicates" type="integer" min="1000" value="1000" label="bootstrap_replicates: Int % Range(1000, None)" help="[default: 1000] The number of bootstrap searches to perform. Minimum of 1000 recomended. "/> + <param name="n_init_pars_trees" type="integer" min="1" optional="true" label="n_init_pars_trees: Int % Range(1, None)" help="[optional] Number of initial parsimony trees. If not set, program defaults will be used. See IQ-TREE manual for details."/> + <param name="n_top_init_trees" type="integer" min="1" optional="true" label="n_top_init_trees: Int % Range(1, None)" help="[optional] Number of top initial trees. If not set, program defaults will be used. See IQ-TREE manual for details."/> + <param name="n_best_retain_trees" type="integer" min="1" optional="true" label="n_best_retain_trees: Int % Range(1, None)" help="[optional] Number of best trees retained during search. If not set, program defaults will be used. See IQ-TREE manual for details."/> + <param name="stop_iter" type="integer" min="1" optional="true" label="stop_iter: Int % Range(1, None)" help="[optional] Number of unsuccessful iterations to stop. If not set, program defaults will be used. See IQ-TREE manual for details."/> + <param name="perturb_nni_strength" type="float" min="0.01" max="0.999999" optional="true" label="perturb_nni_strength: Float % Range(0.01, 1.0)" help="[optional] Perturbation strength for randomized NNI. If not set, program defaults will be used. See IQ-TREE manual for details."/> + <param name="spr_radius" type="integer" min="1" optional="true" label="spr_radius: Int % Range(1, None)" help="[optional] Radius for parsimony SPR search. If not set, program defaults will be used. See IQ-TREE manual for details."/> + <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."/> + <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."/> + <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."/> + <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."/> + <param name="allnni" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="allnni: Bool" help="[default: No] Perform more thorough NNI search."/> + <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."/> + <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."/> + <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."/> + <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."/> + <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."/> + </section> + </inputs> + <outputs> + <data name="tree" format="qza" label="${tool.name} on ${on_string}: tree.qza" from_work_dir="tree.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: phylogeny iqtree-ultrafast-bootstrap +============================================= +Construct a phylogenetic tree with IQ-TREE with bootstrap supports. + + +Outputs: +-------- +:tree.qza: The resulting phylogenetic tree. + +| + +Description: +------------ +Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with automatic model selection and bootstrap supports. + + +| + +</help> + <citations> + <citation type="doi">10.1093/molbev/msaa015</citation> + <citation type="doi">10.1038/nmeth.4285</citation> + <citation type="doi">10.1093/molbev/mst024</citation> + <citation type="doi">10.1093/molbev/msx281</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>