alpha: Alpha diversity¶

Docstring:

Usage: qiime diversity alpha [OPTIONS]

  Computes a user-specified alpha diversity metric for all samples in a
  feature table.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
    PresenceAbsence]      The feature table containing the samples for which
                          alpha diversity should be computed.       [required]
Parameters:
  --p-metric TEXT Choices('ace', 'berger_parker_d', 'brillouin_d', 'chao1',
    'chao1_ci', 'dominance', 'doubles', 'enspie', 'esty_ci', 'fisher_alpha',
    'gini_index', 'goods_coverage', 'heip_e', 'kempton_taylor_q',
    'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick',
    'michaelis_menten_fit', 'observed_features', 'osd', 'pielou_e', 'robbins',
    'shannon', 'simpson', 'simpson_e', 'singles', 'strong')
                          The alpha diversity metric to be computed.
                          Information about specific metrics is available at
                          https://data.qiime2.org/a_diversity_metrics
                                                                    [required]
Outputs:
  --o-alpha-diversity ARTIFACT SampleData[AlphaDiversity]
                          Vector containing per-sample alpha diversities.
                                                                    [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.