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.
