faith-pd: Faith’s Phylogenetic Diversity¶

Docstring:

Usage: qiime diversity-lib faith-pd [OPTIONS]

  Computes Faith's Phylogenetic Diversity for all samples in a feature table.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
    PresenceAbsence]      The feature table containing the samples for which
                          Faith's phylogenetic diversity should be computed.
                          Table values will be converted to presence/absence.
                                                                    [required]
  --i-phylogeny ARTIFACT  Phylogenetic tree containing tip identifiers that
    Phylogeny[Rooted]     correspond to the feature identifiers in the table.
                          This tree can contain tip ids that are not present
                          in the table, but all feature ids in the table must
                          be present in this tree.                  [required]
Parameters:
  --p-threads NTHREADS    The number of CPU threads to use in performing this
                          calculation. May not exceed the number of available
                          physical cores. If threads = 'auto', one thread will
                          be created for each identified CPU core on the host.
                                                                  [default: 1]
Outputs:
  --o-vector ARTIFACT SampleData[AlphaDiversity]
                          Vector containing per-sample values for Faith's
                          Phylogenetic Diversity.                   [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: basic
  qiime diversity-lib faith-pd \
    --i-table feature-table.qza \
    --i-phylogeny phylogeny.qza \
    --o-vector faith-pd-vector.qza