<?xml version="1.0" ?>
<tool id="qiime_phylogeny_raxml-rapid-bootstrap" name="qiime phylogeny raxml-rapid-bootstrap"
      version="2020.8">
  <description>Construct a phylogenetic tree with bootstrap supports using RAxML.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime phylogeny raxml-rapid-bootstrap

--i-alignment=$ialignment

#if str($pseed):
  --p-seed=$pseed
#end if
#if str($prapidbootstrapseed):
  --p-rapid-bootstrap-seed=$prapidbootstrapseed
#end if
--p-bootstrap-replicates=$pbootstrapreplicates

--p-n-threads=$pnthreads

#if str($praxmlversion) != 'None':
--p-raxml-version=$praxmlversion
#end if

#if str($psubstitutionmodel) != 'None':
--p-substitution-model=$psubstitutionmodel
#end if

--o-tree=otree

#if str($examples) != 'None':
--examples=$examples
#end if

;
cp otree.qza $otree

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction.                           [required]" name="ialignment" optional="False" type="data" />
    <param label="--p-seed: INTEGER        Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen. [optional]" name="pseed" optional="False" type="text" />
    <param label="--p-rapid-bootstrap-seed: INTEGER Specify a random seed for rapid bootstrapping. This allows you to reproduce rapid bootstrap results. If not supplied then one will be randomly chosen. [optional]" name="prapidbootstrapseed" optional="False" type="text" />
    <param label="--p-bootstrap-replicates: INTEGER Range(10, None)       The number of bootstrap searches to perform. [default: 100]" min="10" name="pbootstrapreplicates" optional="True" type="integer" value="100" />
    <param label="--p-raxml-version: " name="praxmlversion" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="Standard">Standard</option>
      <option value="SSE3">SSE3</option>
      <option value="AVX2">AVX2</option>
    </param>
    <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="GTRGAMMA">GTRGAMMA</option>
      <option value="GTRGAMMAI">GTRGAMMAI</option>
      <option value="GTRCAT">GTRCAT</option>
      <option value="GTRCATI">GTRCATI</option>
    </param>
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="qza" label="${tool.name} on ${on_string}: tree.qza" name="otree" />
    
  </outputs>

  <help><![CDATA[
Construct a phylogenetic tree with bootstrap supports using RAxML.
###############################################################

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

Parameters
----------
alignment : FeatureData[AlignedSequence]
    Aligned sequences to be used for phylogenetic reconstruction.
seed : Int, 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.
rapid_bootstrap_seed : Int, 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.
bootstrap_replicates : Int % Range(10, None), optional
    The number of bootstrap searches to perform.
n_threads : Int % Range(1, None), optional
    The number of threads to use for multithreaded processing. Using more
    than one thread will enable the PTHREADS version of RAxML.
raxml_version : Str % Choices('Standard', 'SSE3', 'AVX2'), optional
    Select a specific CPU optimization of RAxML to use. The SSE3 versions
    will run approximately 40% faster than the standard version. The AVX2
    version will run 10-30% faster than the SSE3 version.
substitution_model : Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI'), optional
    Model of Nucleotide Substitution

Returns
-------
tree : Phylogeny[Unrooted]
    The resulting phylogenetic tree.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>