evaluate-taxonomy: Compute summary statistics on taxonomy artifact(s).¶

Docstring:

Usage: qiime rescript evaluate-taxonomy [OPTIONS]

  Compute summary statistics on taxonomy artifact(s) and visualize as
  interactive lineplots. Summary statistics include the number of unique
  labels, taxonomic entropy, and the number of features that are
  (un)classified at each taxonomic level. This action is useful for both
  reference taxonomies and classification results. The x-axis in these plots
  represents the taxonomic levels present in the input taxonomies so are
  labeled numerically instead of by rank, but typically for 7-level taxonomies
  these will represent: 1 = domain/kingdom, 2 = phylum, 3 = class, 4 = order,
  5 = family, 6 = genus, 7 = species.

Inputs:
  --i-taxonomies ARTIFACTS... List[FeatureData[Taxonomy]]
                          One or more taxonomies to evaluate.       [required]
Parameters:
  --p-labels TEXT...      List of labels to use for labeling evaluation
    List[Str]             results in the resulting visualization. Inputs are
                          labeled with labels in the order that each is input.
                          If there are fewer labels than inputs (or no
                          labels), unnamed inputs are labeled numerically in
                          sequential order. Extra labels are ignored.
                                                                    [optional]
  --p-rank-handle-regex TEXT
                          Regular expression indicating which taxonomic rank
                          a label belongs to; this handle is stripped from the
                          label prior to operating on the taxonomy. The net
                          effect is that ambiguous or empty levels can be
                          removed prior to comparison, enabling selection of
                          taxonomies with more complete taxonomic information.
                          For example, "^[dkpcofgs]__" will recognize
                          greengenes or silva rank handles.         [optional]
Outputs:
  --o-taxonomy-stats VISUALIZATION
                                                                    [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.