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filter-taxa: Filter taxonomy by list of IDs or search criteria.

Docstring:

Usage: qiime rescript filter-taxa [OPTIONS]

  Filter taxonomy by list of IDs or search criteria.

Inputs:
  --i-taxonomy ARTIFACT FeatureData[Taxonomy]
                         Taxonomy to filter.                        [required]
Parameters:
  --m-ids-to-keep-file METADATA...
    (multiple            List of IDs to keep (as Metadata). Selecting these
     arguments will be   IDs occurs after inclusion and exclusion filtering.
     merged)                                                        [optional]
  --p-include TEXT...    List of search terms. Taxa containing one or more of
    List[Str]            these terms will be retained. Inclusion filtering
                         occurs prior to exclusion filtering and selecting
                         `ids-to-keep`.                             [optional]
  --p-exclude TEXT...    List of search terms. Taxa containing one or more of
    List[Str]            these terms will be excluded. Exclusion filtering
                         occurs after inclusion filtering and prior to
                         selecting `ids-to-keep`.                   [optional]
Outputs:
  --o-filtered-taxonomy ARTIFACT FeatureData[Taxonomy]
                         The filtered 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.

Import:

from qiime2.plugins.rescript.methods import filter_taxa

Docstring:

Filter taxonomy by list of IDs or search criteria.

Filter taxonomy by list of IDs or search criteria.

Parameters
----------
taxonomy : FeatureData[Taxonomy]
    Taxonomy to filter.
ids_to_keep : Metadata, optional
    List of IDs to keep (as Metadata). Selecting these IDs occurs after
    inclusion and exclusion filtering.
include : List[Str], optional
    List of search terms. Taxa containing one or more of these terms will
    be retained. Inclusion filtering occurs prior to exclusion filtering
    and selecting `ids_to_keep`.
exclude : List[Str], optional
    List of search terms. Taxa containing one or more of these terms will
    be excluded. Exclusion filtering occurs after inclusion filtering and
    prior to selecting `ids_to_keep`.

Returns
-------
filtered_taxonomy : FeatureData[Taxonomy]
    The filtered taxonomy.