<?xml version="1.0" ?>
<tool id="qiime_alignment_mafft" name="qiime alignment mafft" version="2018.4">
	<description> - De novo multiple sequence alignment with MAFFT</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
 
  qiime alignment mafft --i-sequences=$isequences
  #set $pnthreads = '${GALAXY_SLOTS:-4}'

  #if str($pnthreads):
   --p-n-threads="$pnthreads"
  #end if

  #if str($cmdconfig) != 'None':
   --cmd-config=$cmdconfig
  #end if
  
   --o-alignment=oalignment;
   
   cp oalignment.qza $oalignment

]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-sequences: FeatureData[Sequence] - The sequences to be aligned.  [required]" name="isequences" optional="False" type="data"/>
		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" 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.

Returns
-------
alignment : FeatureData[AlignedSequence]
    The aligned sequences.
 ]]>
</help>
</tool>