Docstring:
Usage: qiime demux filter-samples [OPTIONS]
Filter samples indicated in given metadata out of demultiplexed data.
Specific samples can be further selected with the WHERE clause, and the
`exclude_ids` parameter allows for filtering of all samples not specified.
Inputs:
--i-demux ARTIFACT SampleData[SequencesWithQuality¹ |
PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
The demultiplexed data from which samples should be
filtered. [required]
Parameters:
--m-metadata-file METADATA...
(multiple Sample metadata indicating which sample ids to
arguments will be filter. The optional `where` parameter may be used to
merged) filter ids based on specified conditions in the
metadata. The optional `exclude-ids` parameter may be
used to exclude the ids specified in the metadata
from the filter. [required]
--p-where TEXT Optional SQLite WHERE clause specifying sample
metadata criteria that must be met to be included in
the filtered data. If not provided, all samples in
`metadata` that are also in the demultiplexed data
will be retained. [optional]
--p-exclude-ids / --p-no-exclude-ids
Defaults to False. If True, the samples selected by
the `metadata` and optional `where` parameter will be
excluded from the filtered data. [default: False]
Outputs:
--o-filtered-demux ARTIFACT SampleData[SequencesWithQuality¹ |
PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
Filtered demultiplexed data. [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.demux.methods import filter_samples
Docstring:
Filter samples out of demultiplexed data.
Filter samples indicated in given metadata out of demultiplexed data.
Specific samples can be further selected with the WHERE clause, and the
`exclude_ids` parameter allows for filtering of all samples not specified.
Parameters
----------
demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
The demultiplexed data from which samples should be filtered.
metadata : Metadata
Sample metadata indicating which sample ids to filter. The optional
`where` parameter may be used to filter ids based on specified
conditions in the metadata. The optional `exclude_ids` parameter may be
used to exclude the ids specified in the metadata from the filter.
where : Str, optional
Optional SQLite WHERE clause specifying sample metadata criteria that
must be met to be included in the filtered data. If not provided, all
samples in `metadata` that are also in the demultiplexed data will be
retained.
exclude_ids : Bool, optional
Defaults to False. If True, the samples selected by the `metadata` and
optional `where` parameter will be excluded from the filtered data.
Returns
-------
filtered_demux : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]
Filtered demultiplexed data.
