summarize-plus: Summarize table plus¶

Docstring:

Usage: qiime feature-table summarize-plus [OPTIONS]

  Generate visual and tabular summaries of a feature table. Tabulate sample
  and feature frequencies.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency | PresenceAbsence]
                          The feature table to be summarized.       [required]
Parameters:
  --m-metadata-file METADATA...
    (multiple arguments   The sample metadata.
     will be merged)                                                [optional]
Outputs:
  --o-feature-frequencies ARTIFACT
    ImmutableMetadata     Per-sample and total frequencies per feature.
                                                                    [required]
  --o-sample-frequencies ARTIFACT
    ImmutableMetadata     Observed feature count and total frequencies per
                          sample.                                   [required]
  --o-summary VISUALIZATION
                          Visual summary of feature table           [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.

Examples:
  # ### example: feature table summarize plus
  qiime feature-table summarize-plus \
    --i-table feature-table.qza \
    --o-feature-frequencies feature-frequencies.qza \
    --o-sample-frequencies sample-frequencies.qza \
    --o-summary visual summary.qzv