classify-sklearn: Pre-fitted sklearn-based taxonomy classifier¶

Docstring:

Usage: qiime feature-classifier classify-sklearn [OPTIONS]

  Classify reads by taxon using a fitted classifier.

Inputs:
  --i-reads ARTIFACT FeatureData[Sequence]
                         The feature data to be classified.         [required]
  --i-classifier ARTIFACT
    TaxonomicClassifier  The taxonomic classifier for classifying the reads.
                                                                    [required]
Parameters:
  --p-reads-per-batch VALUE Int % Range(1, None) | Str % Choices('auto')
                         Number of reads to process in each batch. If "auto",
                         this parameter is autoscaled to min( number of query
                         sequences / n-jobs, 20000).         [default: 'auto']
  --p-n-jobs NTHREADS    The maximum number of concurrent worker processes.
                         If 0 all CPUs are used. If 1 is given, no parallel
                         computing code is used at all, which is useful for
                         debugging.                               [default: 1]
  --p-pre-dispatch TEXT  "all" or expression, as in "3*n_jobs". The number of
                         batches (of tasks) to be pre-dispatched.
                                                         [default: '2*n_jobs']
  --p-confidence VALUE Float % Range(0, 1, inclusive_end=True) | Str %
    Choices('disable')   Confidence threshold for limiting taxonomic depth.
                         Set to "disable" to disable confidence calculation,
                         or 0 to calculate confidence but not apply it to
                         limit the taxonomic depth of the assignments.
                                                                [default: 0.7]
  --p-read-orientation TEXT Choices('same', 'reverse-complement', 'auto')
                         Direction of reads with respect to reference
                         sequences. same will cause reads to be classified
                         unchanged; reverse-complement will cause reads to be
                         reversed and complemented prior to classification.
                         "auto" will autodetect orientation based on the
                         confidence estimates for the first 100 reads.
                                                             [default: 'auto']
Outputs:
  --o-classification ARTIFACT FeatureData[Taxonomy]
                                                                    [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.