<?xml version="1.0" ?>
<tool id="qiime_alignment_mafft" name="qiime alignment mafft"
      version="2020.8">
  <description>De novo multiple sequence alignment with MAFFT</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime alignment mafft

--i-sequences=$isequences

#if str($pnthreads) != 'None':
--p-n-threads=$pnthreads
#end if

#if $pparttree:
 --p-parttree
#end if

--o-alignment=oalignment

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

;
cp oalignment.qza $oalignment

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be aligned.              [required]" name="isequences" 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="--p-parttree: --p-parttree: / --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default                             [default: False]" name="pparttree" selected="False" type="boolean" />
    <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}: alignment.qza" name="oalignment" />
    
  </outputs>

  <help><![CDATA[
De novo multiple sequence alignment with MAFFT
###############################################################

Perform de novo multiple sequence alignment using MAFFT.

Parameters
----------
sequences : FeatureData[Sequence]
    The sequences to be aligned.
n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
    The number of threads. (Use `auto` to automatically use all available
    cores)
parttree : Bool, optional
    This flag is required if the number of sequences being aligned are
    larger than 1000000. Disabled by default

Returns
-------
alignment : FeatureData[AlignedSequence]
    The aligned sequences.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>