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 NTHREADS     [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]
  --p-ignore-missing-samples / --p-no-ignore-missing-samples
                          If set to `True` samples and features without
                          metadata are included by setting all metadata values
                          to: "This element has no metadata". By default an
                          exception will be raised if missing elements are
                          encountered. Note, this flag only takes effect if
                          there is at least one overlapping element.
                                                              [default: False]
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.
  --example-data PATH     Write example data and exit.
  --citations             Show citations and exit.
  --use-cache DIRECTORY   Specify the cache to be used for the intermediate
                          work of this action. 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.
  --help                  Show this message and exit.