core-metrics-phylogenetic: Core diversity metrics (phylogenetic and non-phylogenetic)¶

Docstring:

Usage: qiime diversity core-metrics-phylogenetic [OPTIONS]

  Applies a collection of diversity metrics (both phylogenetic and non-
  phylogenetic) to a feature table.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                          The feature table containing the samples over which
                          diversity metrics should be computed.     [required]
  --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]
Parameters:
  --p-sampling-depth INTEGER
    Range(1, None)        The total frequency that each sample should be
                          rarefied to prior to computing diversity metrics.
                                                                    [required]
  --m-metadata-file METADATA...
    (multiple arguments   The sample metadata to use in the emperor plots.
     will be merged)                                                [required]
  --p-with-replacement / --p-no-with-replacement
                          Rarefy with replacement by sampling from the
                          multinomial distribution instead of rarefying
                          without replacement.                [default: False]
  --p-n-jobs-or-threads VALUE Int % Range(1, None) | Str % Choices('auto')
                          [beta/beta-phylogenetic methods only] - The number
                          of concurrent jobs or CPU threads to use in
                          performing this calculation. Individual methods will
                          create jobs/threads as implemented in
                          q2-diversity-lib dependencies. May not exceed the
                          number of available physical cores. If
                          n-jobs-or-threads = 'auto', one thread/job will be
                          created for each identified CPU core on the host.
                                                                  [default: 1]
Outputs:
  --o-rarefied-table ARTIFACT FeatureTable[Frequency]
                          The resulting rarefied feature table.     [required]
  --o-faith-pd-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector of Faith PD values by sample.      [required]
  --o-observed-features-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector of Observed Features values by sample.
                                                                    [required]
  --o-shannon-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector of Shannon diversity values by sample.
                                                                    [required]
  --o-evenness-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector of Pielou's evenness values by sample.
                                                                    [required]
  --o-unweighted-unifrac-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of unweighted UniFrac distances between
                          pairs of samples.                         [required]
  --o-weighted-unifrac-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of weighted UniFrac distances between pairs
                          of samples.                               [required]
  --o-jaccard-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of Jaccard distances between pairs of
                          samples.                                  [required]
  --o-bray-curtis-distance-matrix ARTIFACT
    DistanceMatrix        Matrix of Bray-Curtis distances between pairs of
                          samples.                                  [required]
  --o-unweighted-unifrac-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from unweighted UniFrac
                          distances between samples.                [required]
  --o-weighted-unifrac-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from weighted UniFrac
                          distances between samples.                [required]
  --o-jaccard-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from Jaccard distances between
                          samples.                                  [required]
  --o-bray-curtis-pcoa-results ARTIFACT
    PCoAResults           PCoA matrix computed from Bray-Curtis distances
                          between samples.                          [required]
  --o-unweighted-unifrac-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          unweighted UniFrac.                       [required]
  --o-weighted-unifrac-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          weighted UniFrac.                         [required]
  --o-jaccard-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          Jaccard.                                  [required]
  --o-bray-curtis-emperor VISUALIZATION
                          Emperor plot of the PCoA matrix computed from
                          Bray-Curtis.                              [required]
Miscellaneous:
  --output-dir PATH       Output unspecified results to a directory
  --verbose / --quiet     Display verbose output to stdout and/or stderr
                          during execution of this action. Or silence output
                          if execution is successful (silence is golden).
  --example-data PATH     Write example data and exit.
  --citations             Show citations and exit.
  --help                  Show this message and exit.