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

Docstring:

Usage: qiime diversity core-metrics [OPTIONS]

  Applies a collection of diversity metrics (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]
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 VALUE Int % Range(1, None) | Str % Choices('auto')
                          [beta methods only] - 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.        [default: 1]
Outputs:
  --o-rarefied-table ARTIFACT FeatureTable[Frequency]
                          The resulting rarefied feature table.     [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-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-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-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).
  --recycle-pool TEXT     Use a cache pool for pipeline resumption. QIIME 2
                          will cache your results in this pool for reuse by
                          future invocations. These pool are retained until
                          deleted by the user. If not provided, QIIME 2 will
                          create a pool which is automatically reused by
                          invocations of the same action and removed if the
                          action is successful. Note: these pools are local to
                          the cache you are using.
  --no-recycle            Do not recycle results from a previous failed
                          pipeline run or save the results from this run for
                          future recycling.
  --parallel              Execute your action in parallel. This flag will use
                          your default parallel config.
  --parallel-config FILE  Execute your action in parallel using a config at
                          the indicated path.
  --use-cache DIRECTORY   Specify the cache to be used for the intermediate
                          work of this pipeline. If not provided, the default
                          cache under $TMP/qiime2/ will be used.
                          IMPORTANT FOR HPC USERS: If you are on an HPC system
                          and are using parallel execution it is important to
                          set this to a location that is globally accessible
                          to all nodes in the cluster.
  --example-data PATH     Write example data and exit.
  --citations             Show citations and exit.
  --help                  Show this message and exit.