view qiime2/qiime_diversity_alpha-phylogenetic.xml @ 15:276ec629f09a draft

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

--i-table=$itable

--i-phylogeny=$iphylogeny

--p-metric=$pmetric

--o-alpha-diversity=oalphadiversity

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

;
cp oalphadiversity.qza $oalphadiversity

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]      The feature table containing the samples for which alpha 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="faith_pd">faith_pd</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}: alphadiversity.qza" name="oalphadiversity" />
    
  </outputs>

  <help><![CDATA[
Alpha diversity (phylogenetic)
###############################################################

Computes a user-specified phylogenetic alpha diversity metric for all
samples in a feature table.

Parameters
----------
table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
    The feature table containing the samples for which alpha 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('faith_pd')
    The alpha diversity metric to be computed.

Returns
-------
alpha_diversity : SampleData[AlphaDiversity]
    Vector containing per-sample alpha diversities.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>