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:
Path to the output folder where to save the results
--output actually the output
basename of the path, and
--output_folder is the
dirname of the output path, or are
--output_folder redundant, or something else?
Also, it appears that phylophlan uses
os.mkdir() instead of
os.makedirs(), so the user cannot generated a new, nested directory structure for the output.
Hi there, sorry for the confusion about this. So, the idea is that
--output takes the name of the output directory (but not a path), while instead
--output_folder allows you to set a path where to store the output folder (if not set the output directory from
--output will be created in the current local folder
We can improve the descriptions of those options.
Thanks @f.asnicar for the explanation! Yeah, it might be best to clarify a bit in the CLI docs.