comparison qiime2/qiime_diversity_beta.xml @ 0:370e0b6e9826 draft

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0:370e0b6e9826

<?xml version="1.0" ?>
<tool id="qiime_diversity_beta" name="qiime diversity beta" version="2019.4">
	<description> - Beta diversity</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime diversity beta

--i-table=$itable
--p-metric=$pmetric

#if $ppseudocount:
 --p-pseudocount=$ppseudocount
#end if

#set $pnjobs = '${GALAXY_SLOTS:-4}'
#if str($pnjobs):
 --p-n-jobs="$pnjobs"
#end if

--o-distance-matrix=odistancematrix
;
cp odistancematrix.qza $odistancematrix
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which beta diversity should be computed.           [required]" name="itable" optional="False" type="data"/>
		<param label="--p-metric: " name="pmetric" optional="False" type="select">
			<option value="kulsinski">kulsinski</option>
			<option value="wminkowski">wminkowski</option>
			<option value="correlation">correlation</option>
			<option value="hamming">hamming</option>
			<option value="canberra">canberra</option>
			<option value="canberra_adkins">canberra_adkins</option>
			<option value="sqeuclidean">sqeuclidean</option>
			<option value="sokalmichener">sokalmichener</option>
			<option value="cityblock">cityblock</option>
			<option value="braycurtis">braycurtis</option>
			<option value="matching">matching</option>
			<option value="russellrao">russellrao</option>
			<option value="cosine">cosine</option>
			<option value="yule">yule</option>
			<option value="euclidean">euclidean</option>
			<option value="rogerstanimoto">rogerstanimoto</option>
			<option value="seuclidean">seuclidean</option>
			<option value="jaccard">jaccard</option>
			<option value="sokalsneath">sokalsneath</option>
			<option value="aitchison">aitchison</option>
			<option value="chebyshev">chebyshev</option>
			<option value="dice">dice</option>
			<option value="mahalanobis">mahalanobis</option>
		</param>
		<param label="--p-pseudocount: INTEGER Range(1, None)     A pseudocount to handle zeros for compositional metrics.  This is ignored for other metrics. [default: 1]" name="ppseudocount" optional="True" type="integer" min="1" value="1"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: distancematrix.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('sokalmichener', 'yule', 'russellrao', 'rogerstanimoto', 'aitchison', 'correlation', 'jaccard', 'cosine', 'euclidean', 'sqeuclidean', 'chebyshev', 'cityblock', 'matching', 'dice', 'mahalanobis', 'wminkowski', 'kulsinski', 'seuclidean', 'sokalsneath', 'canberra', 'canberra_adkins', 'hamming', 'braycurtis')
    The beta diversity metric to be computed.
pseudocount : Int % Range(1, None), optional
    A pseudocount to handle zeros for compositional metrics.  This is
    ignored for other metrics.

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