<?xml version="1.0" ?>
<tool id="qiime_diversity_beta" name="qiime diversity beta" version="2018.4">
	<description> - Beta diversity</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
  qiime diversity beta --i-table=$itable --p-metric=$pmetric --o-distance-matrix=odistancematrix
  
  #if str($cmdconfig) != 'None':
   --cmd-config=$cmdconfig
  #end if
  
  #set $pnjobs = '${GALAXY_SLOTS:-4}'
  
  #if str($pnjobs):
   --p-n-jobs="$pnjobs"
  #end if
  
  ;
  cp odistancematrix.qza $odistancematrix;
  ]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table containing the samples over which beta diversity should be computed.  [required]" name="itable" optional="False" type="data"/>

		<param label="--p-metric:  The beta diversity metric to be computed.
                                  [required]" name="pmetric" optional="False" type="select" >
			<option value="hamming">hamming</option>
			<option value="sqeuclidean">sqeuclidean</option>
			<option value="cityblock">cityblock</option>
			<option value="sokalmichener">sokalmichener</option>
			<option value="braycurtis">braycurtis</option>
			<option value="cosine">cosine</option>
			<option value="euclidean">euclidean</option>
			<option value="rogerstanimoto">rogerstanimoto</option>
			<option value="canberra">canberra</option>
			<option value="seuclidean">seuclidean</option>
			<option value="correlation">correlation</option>
			<option value="sokalsneath">sokalsneath</option>
			<option value="chebyshev">chebyshev</option>
			<option value="mahalanobis">mahalanobis</option>
			<option value="matching">matching</option>
			<option value="kulsinski">kulsinski</option>
			<option value="yule">yule</option>
			<option value="dice">dice</option>
			<option value="russellrao">russellrao</option>
			<option value="wminkowski">wminkowski</option>
			<option value="jaccard">jaccard</option>
		</param>
		
		<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}: distance-matrix.qza" name="odistancematrix"/>
	</outputs>
	<help><![CDATA[
Beta diversity
--------------

Computes a user-specified beta diversity metric for all pairs of samples in
a feature table.

Parameters
----------
table : FeatureTable[Frequency]
    The feature table containing the samples over which beta diversity
    should be computed.
metric : Str % Choices({'braycurtis', 'canberra', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'kulsinski', 'mahalanobis', 'matching', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'wminkowski', 'yule'})
    The beta diversity metric to be computed.

Returns
-------
distance_matrix : DistanceMatrix
    The resulting distance matrix.
    ]]>
	</help>
<macros>
	<import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation" />
</tool>