annotate qiime2/qiime_diversity_beta-phylogenetic.xml @ 15:276ec629f09a draft

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

--i-table=$itable

--i-phylogeny=$iphylogeny

--p-metric=$pmetric

#if str($pthreads) != 'None':
--p-threads=$pthreads
#end if

#if $pvarianceadjusted:
 --p-variance-adjusted
#end if

#if str($palpha):
  --p-alpha=$palpha
#end if
#if $pbypasstips:
 --p-bypass-tips
#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 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="weighted_unifrac">weighted_unifrac</option>
      <option value="unweighted_unifrac">unweighted_unifrac</option>
      <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
      <option value="generalized_unifrac">generalized_unifrac</option>
    </param>
    <param label="--p-threads: " name="pthreads" 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="--p-variance-adjusted: --p-variance-adjusted: / --p-no-variance-adjusted Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.                         [default: False]" name="pvarianceadjusted" selected="False" type="boolean" />
    <param label="--p-alpha: PROPORTION Range(0, 1, inclusive_end=True) This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.             [optional]" name="palpha" optional="False" type="text" />
    <param label="--p-bypass-tips: --p-bypass-tips: / --p-no-bypass-tips In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs                                [default: False]" name="pbypasstips" selected="False" type="boolean" />
    <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 (phylogenetic)
###############################################################

Computes a user-specified phylogenetic 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.
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('generalized_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac', 'unweighted_unifrac')
    The beta diversity metric to be computed.
threads : Int % Range(1, None) | Str % Choices('auto'), optional
    The number of CPU threads to use in performing this calculation. May
    not exceed the number of available physical cores. If threads = 'auto',
    one thread will be created for each identified CPU core on the host.
variance_adjusted : Bool, optional
    Perform variance adjustment based on Chang et al. BMC Bioinformatics
    2011. Weights distances based on the proportion of the relative
    abundance represented between the samples at a given node under
    evaluation.
alpha : Float % Range(0, 1, inclusive_end=True), optional
    This parameter is only used when the choice of metric is
    generalized_unifrac. The value of alpha controls importance of sample
    proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to
    unweighted UniFrac, but only if the sample proportions are
    dichotomized.
bypass_tips : Bool, optional
    In a bifurcating tree, the tips make up about 50% of the nodes in a
    tree. By ignoring them, specificity can be traded for reduced compute
    time. This has the effect of collapsing the phylogeny, and is analogous
    (in concept) to moving from 99% to 97% OTUs

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