Docstring:
Usage: qiime metadata merge [OPTIONS]
Merge metadata that contains overlapping ids or overlapping columns, but not
both overlapping ids and overlapping columns. The result will be the union
(i.e., outer join) of the ids and columns from the two metadata inputs.
Attemping to merge metadata with both overlapping ids and overlapping
columns will currently fail because we don't resolve conflicting column
values for a sample. Merging metadata with neither overlapping ids or
overlapping columns is possible with this action.
To merge more than two metadata objects, run this command multiple times,
iteratively using the output of the previous run as one of the metadata
inputs.
The output, an ImmutableMetadata artifact, can be used anywhere that a
metadata file can be used, or can be exported to a metadata tsv file in the
typical format.
Parameters:
--m-metadata1-file METADATA...
(multiple First metadata file to merge.
arguments will be
merged) [required]
--m-metadata2-file METADATA...
(multiple Second metadata file to merge.
arguments will be
merged) [required]
Outputs:
--o-merged-metadata ARTIFACT
ImmutableMetadata The merged metadata. [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.metadata.methods import merge
Docstring:
Merge metadata
Merge metadata that contains overlapping ids or overlapping columns, but
not both overlapping ids and overlapping columns. The result will be the
union (i.e., outer join) of the ids and columns from the two metadata
inputs. Attemping to merge metadata with both overlapping ids and
overlapping columns will currently fail because we don't resolve
conflicting column values for a sample. Merging metadata with neither
overlapping ids or overlapping columns is possible with this action. To
merge more than two metadata objects, run this command multiple times,
iteratively using the output of the previous run as one of the metadata
inputs. The output, an ImmutableMetadata artifact, can be used anywhere
that a metadata file can be used, or can be exported to a metadata tsv file
in the typical format.
Parameters
----------
metadata1 : Metadata
First metadata file to merge.
metadata2 : Metadata
Second metadata file to merge.
Returns
-------
merged_metadata : ImmutableMetadata
The merged metadata.
