<?xml version="1.0" ?>
<tool id="qiime_alignment_mafft-add" name="qiime alignment mafft-add"
      version="2020.8">
  <description>Add sequences to multiple sequence alignment with MAFFT.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime alignment mafft-add

--i-alignment=$ialignment

--i-sequences=$isequences

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

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

--o-expanded-alignment=oexpandedalignment

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

;
cp oexpandedalignment.qza $oexpandedalignment

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] The alignment to which sequences should be added. [required]" name="ialignment" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be added.                [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}: expandedalignment.qza" name="oexpandedalignment" />
    
  </outputs>

  <help><![CDATA[
Add sequences to multiple sequence alignment with MAFFT.
###############################################################

Add new sequences to an existing alignment with MAFFT.

Parameters
----------
alignment : FeatureData[AlignedSequence]
    The alignment to which sequences should be added.
sequences : FeatureData[Sequence]
    The sequences to be added.
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
-------
expanded_alignment : FeatureData[AlignedSequence]
    Alignment containing the provided aligned and unaligned sequences.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>