beta: Beta diversity¶

Docstring:

Usage: qiime diversity beta [OPTIONS]

  Computes a user-specified beta diversity metric for all pairs of samples in
  a feature table.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
    PresenceAbsence]      The feature table containing the samples over which
                          beta diversity should be computed.        [required]
Parameters:
  --p-metric TEXT Choices('aitchison', 'braycurtis', 'canberra',
    'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine',
    'dice', 'euclidean', 'hamming', 'jaccard', 'jensenshannon', 'matching',
    'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean',
    'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule')
                          The beta diversity metric to be computed. [required]
  --p-pseudocount INTEGER A pseudocount to handle zeros for compositional
    Range(1, None)        metrics.  This is ignored for other metrics.
                                                                  [default: 1]
  --p-n-jobs NTHREADS     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-distance-matrix ARTIFACT
    DistanceMatrix        The resulting distance matrix.            [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.