view qiime2-2020.8/qiime_diversity_beta.xml @ 20:d93d8888f0b0 draft

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<?xml version="1.0" ?>
<tool id="qiime_diversity_beta" name="qiime diversity beta"
      version="2020.8">
  <description>Beta diversity</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime diversity beta

--i-table=$itable

--p-metric=$pmetric

--p-pseudocount=$ppseudocount

#if str($pnjobs) != 'None':
--p-n-jobs=$pnjobs
#end if

--o-distance-matrix=odistancematrix

#if str($examples) != 'None':
--examples=$examples
#end if

;
cp odistancematrix.qza $odistancematrix

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]   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="braycurtis">braycurtis</option>
      <option value="euclidean">euclidean</option>
      <option value="cityblock">cityblock</option>
      <option value="cosine">cosine</option>
      <option value="minkowski">minkowski</option>
      <option value="matching">matching</option>
      <option value="correlation">correlation</option>
      <option value="russellrao">russellrao</option>
      <option value="sokalsneath">sokalsneath</option>
      <option value="seuclidean">seuclidean</option>
      <option value="canberra">canberra</option>
      <option value="sokalmichener">sokalmichener</option>
      <option value="kulsinski">kulsinski</option>
      <option value="jensenshannon">jensenshannon</option>
      <option value="jaccard">jaccard</option>
      <option value="hamming">hamming</option>
      <option value="chebyshev">chebyshev</option>
      <option value="yule">yule</option>
      <option value="dice">dice</option>
      <option value="sqeuclidean">sqeuclidean</option>
      <option value="aitchison">aitchison</option>
      <option value="canberra_adkins">canberra_adkins</option>
      <option value="rogerstanimoto">rogerstanimoto</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]" min="1" name="ppseudocount" optional="True" type="integer" value="1" />
    <param label="--p-n-jobs: " name="pnjobs" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="Int % Range(1">Int % Range(1</option>
      <option value="None">None</option>
    </param>
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </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 | RelativeFrequency | PresenceAbsence]
    The feature table containing the samples over which beta diversity
    should be computed.
metric : Str % Choices('yule', 'cityblock', 'matching', 'russellrao', 'seuclidean', 'jaccard', 'braycurtis', 'minkowski', 'sokalmichener', 'aitchison', 'canberra_adkins', 'euclidean', 'kulsinski', 'cosine', 'sqeuclidean', 'sokalsneath', 'correlation', 'hamming', 'dice', 'rogerstanimoto', 'canberra', 'chebyshev', 'jensenshannon')
    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.
n_jobs : Int % Range(1, None) | Str % Choices('auto'), optional
    The number of concurrent jobs to use in performing this calculation.
    May not exceed the number of available physical cores. If n_jobs =
    'auto', one job will be launched for each identified CPU core on the
    host.

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