<?xml version="1.0" ?>
<tool id="qiime_alignment_mafft" name="qiime alignment mafft" version="2019.4">
	<description> - De novo multiple sequence alignment with MAFFT</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime alignment mafft

--i-sequences=$isequences
--o-alignment=oalignment

#set $pnthreads = '${GALAXY_SLOTS:-4}'

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


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