parse-silva-taxonomy: Generates a SILVA fixed-rank taxonomy.¶

Docstring:

Usage: qiime rescript parse-silva-taxonomy [OPTIONS]

  Parses several files from the SILVA reference database to produce a
  GreenGenes-like fixed rank taxonomy that is 6 or 7 ranks deep, depending on
  whether or not `include_species_labels` is applied. The generated ranks (and
  the rank handles used to label these ranks in the resulting taxonomy) are:
  domain (d__), phylum (p__), class (c__), order (o__), family (f__), genus
  (g__), and species (s__). NOTE: THIS ACTION ACQUIRES DATA FROM THE SILVA
  DATABASE. SEE https://www.arb-silva.de/silva-license-information/ FOR MORE
  INFORMATION and be aware that earlier versions may be released under a
  different license.

Inputs:
  --i-taxonomy-tree ARTIFACT
    Phylogeny[Rooted]    SILVA hierarchical taxonomy tree. The SILVA release
                         filename typically takes the form of:
                         'tax_slv_ssu_X.tre', where 'X' is the SILVA version
                         number.                                    [required]
  --i-taxonomy-map ARTIFACT FeatureData[SILVATaxidMap]
                         SILVA taxonomy map. This file contains a mapping of
                         the sequence accessions to the numeric taxonomy
                         identifiers and species label information. The SILVA
                         release filename is typically in the form of:
                         'taxmap_slv_ssu_ref_X.txt', or
                         'taxmap_slv_ssu_ref_nr_X.txt' where 'X' is the SILVA
                         version number.                            [required]
  --i-taxonomy-ranks ARTIFACT FeatureData[SILVATaxonomy]
                         SILVA taxonomy file. This file contains the
                         taxonomic rank information for each numeric taxonomy
                         identifier and the taxonomy. The SILVA  filename
                         typically takes the form of: 'tax_slv_ssu_X.txt',
                         where 'X' is the SILVA version number.     [required]
Parameters:
  --p-rank-propagation / --p-no-rank-propagation
                         If a rank has no taxonomy associated with it, the
                         taxonomy from the upper-level rank of that lineage,
                         will be propagated downward. For example, if we are
                         missing the genus label for 'f__Pasteurellaceae;
                         g__'then the 'f__' rank will be propagated to become:
                         'f__Pasteurellaceae; g__Pasteurellaceae'.
                                                               [default: True]
  --p-ranks TEXT... Choices('domain', 'superkingdom', 'kingdom',
    'subkingdom', 'superphylum', 'phylum', 'subphylum', 'infraphylum',
    'superclass', 'class', 'subclass', 'infraclass', 'superorder', 'order',
    'suborder', 'superfamily', 'family', 'subfamily', 'genus')
                         List of taxonomic ranks for building a taxonomy from
                         the SILVA Taxonomy database. Use
                         'include-species-labels' to append the organism name
                         as the species label. [default: 'domain', 'phylum',
                         'class', 'order', 'family', 'genus']       [optional]
  --p-include-species-labels / --p-no-include-species-labels
                         Include species rank labels in taxonomy output.
                         Note: species-labels may not be reliable in all
                         cases.                               [default: False]
Outputs:
  --o-taxonomy ARTIFACT FeatureData[Taxonomy]
                         The resulting fixed-rank formatted SILVA taxonomy.
                                                                    [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.