taxpasta standardise --help
Usage: taxpasta standardise [OPTIONS] PROFILE
Standardise a taxonomic profile (alias: 'standardize').
PROFILE A file containing a taxonomic profile. [required]
-p, --profiler [bracken|centrifuge|diamond|ganon|kaiju|kmcp|kraken2|krakenuniq|megan6|metaphlan|motus]
The taxonomic profiler used. [required]
-o, --output PATH The desired output file. By default, the
file extension will be used to determine the
output format, but when setting the format
explicitly using the --output-format option,
automatic detection is disabled. [required]
The desired output format. Depending on the
choice, additional package dependencies may
apply. By default it will be parsed from the
output file name but it can be set
explicitly and will then disable the
--summarise-at, --summarize-at TEXT
Summarise abundance profiles at higher
taxonomic rank. The provided option must
match a rank in the taxonomy exactly. This
is akin to the clade assigned reads provided
by, for example, kraken2, where the
abundances of a whole taxonomic branch are
assigned to a taxon at the desired rank.
Please note that abundances above the
selected rank are simply ignored. No attempt
is made to redistribute those down to the
desired rank. Some tools, like Bracken, were
designed for this purpose but it doesn't
seem like a problem we can generally solve
--taxonomy PATH The path to a directory containing taxdump
files. At least nodes.dmp and names.dmp are
required. A merged.dmp file is optional.
--add-name Add the taxon name to the output.
--add-rank Add the taxon rank to the output.
--add-lineage Add the taxon's entire lineage to the
output. These are taxon names separated by
--add-id-lineage Add the taxon's entire lineage to the
output. These are taxon identifiers
separated by semi-colons.
--add-rank-lineage Add the taxon's entire rank lineage to the
output. These are taxon ranks separated by
-h, --help Show this message and exit.