<?xml version="1.0" ?>
<tool id="qiime_phylogeny_fasttree" name="qiime phylogeny fasttree"
      version="2020.8">
  <description>Construct a phylogenetic tree with FastTree.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime phylogeny fasttree

--i-alignment=$ialignment

#if str($pnthreads) != 'None':
--p-n-threads=$pnthreads
#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-n-threads: " name="pnthreads" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="Int % Range(1">Int % Range(1</option>
      <option value="None">None</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 FastTree.
###############################################################

Construct a phylogenetic tree with FastTree.

Parameters
----------
alignment : FeatureData[AlignedSequence]
    Aligned sequences to be used for phylogenetic reconstruction.
n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
    The number of threads. Using more than one thread runs the non-
    deterministic variant of `FastTree` (`FastTreeMP`), and may result in a
    different tree than single-threading. See
    http://www.microbesonline.org/fasttree/#OpenMP for details. (Use `auto`
    to automatically use all available cores)

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