<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2023, 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: 2022.11.1)
for:
    qiime2 (version: 2022.11.1)
-->
<tool name="qiime2 phylogeny raxml-rapid-bootstrap" id="qiime2__phylogeny__raxml_rapid_bootstrap" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Construct a phylogenetic tree with bootstrap supports using RAxML.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.11</container>
    </requirements>
    <version_command>q2galaxy version phylogeny</version_command>
    <command detect_errors="exit_code">q2galaxy run phylogeny raxml_rapid_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 for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen."/>
            <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."/>
            <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."/>
            <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."/>
            <param name="raxml_version" type="select" label="raxml_version: Str % Choices('Standard', 'SSE3', 'AVX2')" display="radio">
                <option value="Standard" selected="true">Standard</option>
                <option value="SSE3">SSE3</option>
                <option value="AVX2">AVX2</option>
            </param>
            <param name="substitution_model" type="select" label="substitution_model: Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI')" display="radio">
                <option value="GTRGAMMA" selected="true">GTRGAMMA</option>
                <option value="GTRGAMMAI">GTRGAMMAI</option>
                <option value="GTRCAT">GTRCAT</option>
                <option value="GTRCATI">GTRCATI</option>
            </param>
        </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 raxml-rapid-bootstrap
========================================
Construct a phylogenetic tree with bootstrap supports using RAxML.


Outputs:
--------
:tree.qza: The resulting phylogenetic tree.

|  

Description:
------------
Construct a phylogenetic tree with RAxML with the addition of rapid bootstrapping support values. See: https://sco.h-its.org/exelixis/web/software/raxml/


|  

</help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btu033</citation>
        <citation type="doi">10.1080/10635150802429642</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>