<?xml version="1.0" ?>
<tool id="qiime_diversity_alpha-phylogenetic-alt" name="qiime diversity alpha-phylogenetic-alt" version="2019.7">
	<description> - Alpha diversity (phylogenetic) - alternative implementation</description>
	<requirements>
		<requirement type="package" version="2019.7">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime diversity alpha-phylogenetic-alt

--i-table=$itable
--i-phylogeny=$iphylogeny

--p-metric=$pmetric

--o-alpha-diversity=oalphadiversity

;
cp oalphadiversity.qza $oalphadiversity
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples for which alpha diversity should be computed.       [required]" name="itable" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Phylogenetic tree containing tip identifiers that Phylogeny[Rooted]     correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.                  [required]" name="iphylogeny" optional="False" type="data"/>
		<param label="--p-metric: " name="pmetric" optional="False" type="select">
			<option value="faith_pd">faith_pd</option>
		</param>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: alphadiversity.qza" name="oalphadiversity"/>
	</outputs>
	<help><![CDATA[
Alpha diversity (phylogenetic) - alternative implementation
############################################################

Computes a user-specified phylogenetic alpha diversity metric for all
samples in a feature table. This implementation is recommended for large
datasets, otherwise the results are identical to alpha_phylogenetic.   This
method is an implementation of the Stacked Faith Algorithm (manuscript in
preparation).

Parameters
----------
table : FeatureTable[Frequency]
    The feature table containing the samples for which alpha diversity
    should be computed.
phylogeny : Phylogeny[Rooted]
    Phylogenetic tree containing tip identifiers that correspond to the
    feature identifiers in the table. This tree can contain tip ids that
    are not present in the table, but all feature ids in the table must be
    present in this tree.
metric : Str % Choices('faith_pd')
    The alpha diversity metric to be computed.

Returns
-------
alpha_diversity : SampleData[AlphaDiversity] % Properties('phylogenetic')
    Vector containing per-sample alpha diversities.
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>