Docstring:
Usage: qiime feature-table summarize-plus [OPTIONS]
Generate visual and tabular summaries of a feature table. Tabulate sample
and feature frequencies.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency | PresenceAbsence]
The feature table to be summarized. [required]
Parameters:
--m-metadata-file METADATA...
(multiple arguments The sample metadata.
will be merged) [optional]
Outputs:
--o-feature-frequencies ARTIFACT
ImmutableMetadata Per-sample and total frequencies per feature.
[required]
--o-sample-frequencies ARTIFACT
ImmutableMetadata Observed feature count and total frequencies per
sample. [required]
--o-summary VISUALIZATION
Visual summary of feature table [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).
--recycle-pool TEXT Use a cache pool for pipeline resumption. QIIME 2
will cache your results in this pool for reuse by
future invocations. These pool are retained until
deleted by the user. If not provided, QIIME 2 will
create a pool which is automatically reused by
invocations of the same action and removed if the
action is successful. Note: these pools are local to
the cache you are using.
--no-recycle Do not recycle results from a previous failed
pipeline run or save the results from this run for
future recycling.
--parallel Execute your action in parallel. This flag will use
your default parallel config.
--parallel-config FILE Execute your action in parallel using a config at
the indicated path.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this pipeline. 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.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Examples:
# ### example: feature table summarize plus
qiime feature-table summarize-plus \
--i-table feature-table.qza \
--o-feature-frequencies feature-frequencies.qza \
--o-sample-frequencies sample-frequencies.qza \
--o-summary visual summary.qzv
Import:
from qiime2.plugins.feature_table.pipelines import summarize_plus
Docstring:
Summarize table plus
Generate visual and tabular summaries of a feature table. Tabulate sample
and feature frequencies.
Parameters
----------
table : FeatureTable[Frequency | PresenceAbsence]
The feature table to be summarized.
metadata : Metadata, optional
The sample metadata.
Returns
-------
feature_frequencies : ImmutableMetadata
Per-sample and total frequencies per feature.
sample_frequencies : ImmutableMetadata
Observed feature count and total frequencies per sample.
summary : Visualization
Visual summary of feature table
