Docstring:
Usage: qiime diversity filter-distance-matrix [OPTIONS]
Filter samples from a distance matrix, retaining only the samples matching
search criteria specified by `metadata` and `where` parameters (or retaining
only the samples not matching that criteria, if `exclude_ids` is True). See
the filtering tutorial on https://docs.qiime2.org for additional details.
Inputs:
--i-distance-matrix ARTIFACT
DistanceMatrix Distance matrix to filter by sample. [required]
Parameters:
--m-metadata-file METADATA...
(multiple Sample metadata used with `where` parameter when
arguments will be selecting samples to retain, or with `exclude-ids`
merged) when selecting samples to discard. [required]
--p-where TEXT SQLite WHERE clause specifying sample metadata
criteria that must be met to be included in the
filtered distance matrix. If not provided, all
samples in `metadata` that are also in the input
distance matrix will be retained. [optional]
--p-exclude-ids / --p-no-exclude-ids
If `True`, the samples selected by `metadata` or
`where` parameters will be excluded from the filtered
distance matrix instead of being retained.
[default: False]
Outputs:
--o-filtered-distance-matrix ARTIFACT
DistanceMatrix Distance matrix filtered to include samples matching
search criteria [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.diversity.methods import filter_distance_matrix
Docstring:
Filter samples from a distance matrix.
Filter samples from a distance matrix, retaining only the samples matching
search criteria specified by `metadata` and `where` parameters (or
retaining only the samples not matching that criteria, if `exclude_ids` is
True). See the filtering tutorial on https://docs.qiime2.org for additional
details.
Parameters
----------
distance_matrix : DistanceMatrix
Distance matrix to filter by sample.
metadata : Metadata
Sample metadata used with `where` parameter when selecting samples to
retain, or with `exclude_ids` when selecting samples to discard.
where : Str, optional
SQLite WHERE clause specifying sample metadata criteria that must be
met to be included in the filtered distance matrix. If not provided,
all samples in `metadata` that are also in the input distance matrix
will be retained.
exclude_ids : Bool, optional
If `True`, the samples selected by `metadata` or `where` parameters
will be excluded from the filtered distance matrix instead of being
retained.
Returns
-------
filtered_distance_matrix : DistanceMatrix
Distance matrix filtered to include samples matching search criteria
