<?xml version="1.0" ?>
<tool id="qiime_phylogeny_fasttree" name="qiime phylogeny fasttree" version="2018.4">
	<description> - Construct a phylogenetic tree with FastTree.</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
	<![CDATA[
	qiime phylogeny fasttree --i-alignment=$ialignment
	#set $pnthreads = '${GALAXY_SLOTS:-4}'

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

	#if str($cmdconfig) != 'None':
	 --cmd-config=$cmdconfig
	#end if
	 --o-tree=otree;
	cp otree.qza $otree;
	]]>
	</command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-alignment: FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction.  [required]" name="ialignment" optional="False" type="data"/>
		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: 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.

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