edit-taxonomy: Edit taxonomy strings with find and replace terms.¶

Docstring:

Usage: qiime rescript edit-taxonomy [OPTIONS]

  A method that allows the user to edit taxonomy strings. This is often used
  to fix inconsistent and/or inccorect taxonomic annotations. The user can
  either provide two separate lists of strings, i.e. 'search-strings', and
  'replacement-strings', on the command line, and/or a single tab-delimited
  replacement map file containing a list of these strings. In both cases the
  number of search strings must match the number of replacement strings. That
  is the first string in 'search-strings' is replaced with the first string in
  'replacement-strings', and so on. In the case that both search / replacement
  strings, and a replacement map file are provided, they will be merged.

Inputs:
  --i-taxonomy ARTIFACT FeatureData[Taxonomy]
                         Taxonomy strings data to be edited.        [required]
Parameters:
  --m-replacement-map-file METADATA
  --m-replacement-map-column COLUMN  MetadataColumn[Categorical]
                         A tab-delimitad metadata file in which the strings
                         in the 'id' column are replaced by the
                         'replacement-strings' in the second column. All
                         strings in the 'id' column must be unique! [optional]
  --p-search-strings TEXT...
    List[Str]            Only used in conjuntion with 'replacement-strings'.
                         Each string in this list is searched for and replaced
                         with a string in the list of 'replace-ment-strings'.
                         That is the first string in 'search-strings' is
                         replaced with the first string in
                         'replacement-strings', and so on. The number of
                         'search-strings' must be equal to the number of
                         replacement strings.                       [optional]
  --p-replacement-strings TEXT...
    List[Str]            Only used in conjuntion with 'search-strings'. This
                         must contain the same number of replacement strings
                         as search strings. See 'search-strings' parameter
                         text for more details.                     [optional]
  --p-use-regex / --p-no-use-regex
                         Toggle regular expressions. By default, only
                         litereal substring matching is performed.
                                                              [default: False]
Outputs:
  --o-edited-taxonomy ARTIFACT FeatureData[Taxonomy]
                         Taxonomy in which the original strings are replaced
                         by user-supplied strings.                  [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.