annotate qiime2-2020.8/qiime_diversity-lib_unweighted-unifrac.xml @ 20:d93d8888f0b0 draft

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<?xml version="1.0" ?>
<tool id="qiime_diversity-lib_unweighted-unifrac" name="qiime diversity-lib unweighted-unifrac"
      version="2020.8">
  <description>Unweighted Unifrac</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime diversity-lib unweighted-unifrac

--i-table=$itable

--i-phylogeny=$iphylogeny

#if str($pthreads) != 'None':
--p-threads=$pthreads
#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 for which Unweighted Unifrac 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-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-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[
Unweighted Unifrac
###############################################################

Compute Unweighted Unifrac for each sample in a feature table

Parameters
----------
table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
    The feature table containing the samples for which Unweighted Unifrac
    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.
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.
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
    Distance matrix for Unweighted Unifrac.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>