merge: Combine multiple tables¶

Docstring:

Usage: qiime feature-table merge [OPTIONS]

  Combines feature tables using the `overlap_method` provided.

Inputs:
  --i-tables ARTIFACTS... List[FeatureTable[Frequency]¹ |
    FeatureTable[RelativeFrequency]² | FeatureTable[PresenceAbsence]³]
                         The collection of feature tables to be merged.
                                                                    [required]
Parameters:
  --p-overlap-method VALUE Str % Choices('average',
    'error_on_overlapping_feature', 'error_on_overlapping_sample', 'sum')¹ |
    Str % Choices('average', 'error_on_overlapping_feature',
    'error_on_overlapping_sample')² | Str %
    Choices('error_on_overlapping_feature', 'error_on_overlapping_sample',
    'union')³            Method for handling overlapping ids.
                                      [default: 'error_on_overlapping_sample']
Outputs:
  --o-merged-table ARTIFACT FeatureTable[Frequency]¹ |
    FeatureTable[RelativeFrequency]² | FeatureTable[PresenceAbsence]³
                         The resulting merged 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).
  --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.

Examples:
  # ### example: feature table merge two tables
  qiime feature-table merge \
    --i-tables feature-table1.qza feature-table2.qza \
    --o-merged-table merged-table.qza

  # ### example: feature table merge three tables
  qiime feature-table merge \
    --i-tables feature-table1.qza feature-table2.qza feature-table3.qza \
    --p-overlap-method sum \
    --o-merged-table merged-table.qza