beta-passthrough: Beta Passthrough (non-phylogenetic)¶

Docstring:

Usage: qiime diversity-lib beta-passthrough [OPTIONS]

  Computes a distance matrix for all pairs of samples in a feature table using
  the scikit-bio implementation of the selected beta diversity metric.

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

Examples:
  # ### example: run on one core (by default)
  qiime diversity-lib beta-passthrough \
    --i-table feature-table.qza \
    --p-metric euclidean \
    --o-distance-matrix euclidean-dm.qza

  # ### example: to run on n cores, replace 1 here with your preferred integer
  qiime diversity-lib beta-passthrough \
    --i-table feature-table.qza \
    --p-metric euclidean \
    --p-n-jobs 1 \
    --o-distance-matrix euclidean-dm.qza

  # ### example: use 'auto' to run on all of host system's available CPU cores
  # A default pseudocount of 1 is added to feature counts. Pseudocount is
  # ignored for non-compositional metrics.
  qiime diversity-lib beta-passthrough \
    --i-table feature-table.qza \
    --p-metric aitchison \
    --p-n-jobs auto \
    --o-distance-matrix aitchison-dm.qza

  # ### example: use 'pseudocount' to manually set a pseudocount for
  # compositional metrics
  qiime diversity-lib beta-passthrough \
    --i-table feature-table.qza \
    --p-metric aitchison \
    --p-n-jobs auto \
    --p-pseudocount 5 \
    --o-distance-matrix aitchison-dm.qza