The phylophlan v3.0.3 cli help doc states:
-o OUTPUT, --output OUTPUT
Output folder name, otherwise it will be the name of
the input folder concatenated with the name of the
database used (default: None)
…but also states further on:
--output_folder OUTPUT_FOLDER
Path to the output folder where to save the results
(default: )
Is --output
actually the output basename
of the path, and --output_folder
is the dirname
of the output path, or are --output
and --output_folder
redundant, or something else?