collapse: Collapse features by their taxonomy at the specified level¶

Docstring:

Usage: qiime taxa collapse [OPTIONS]

  Collapse groups of features that have the same taxonomic assignment through
  the specified level. The frequencies of all features will be summed when
  they are collapsed.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                         Feature table to be collapsed.             [required]
  --i-taxonomy ARTIFACT FeatureData[Taxonomy]
                         Taxonomic annotations for features in the provided
                         feature table. All features in the feature table must
                         have a corresponding taxonomic annotation. Taxonomic
                         annotations that are not present in the feature table
                         will be ignored.                           [required]
Parameters:
  --p-level INTEGER      The taxonomic level at which the features should be
                         collapsed. All ouput features will have exactly this
                         many levels of taxonomic annotation.       [required]
Outputs:
  --o-collapsed-table ARTIFACT FeatureTable[Frequency]
                         The resulting feature table, where all features are
                         now taxonomic annotations with the user-specified
                         number of levels.                          [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: collapse
  qiime taxa collapse \
    --i-table table.qza \
    --i-taxonomy taxonomy.qza \
    --p-level 6 \
    --o-collapsed-table collapsed-table-l6.qza