Phylophlan3: confusing CLI help docs

Microbial community profiling PhyloPhlAn
1

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?

2

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.

3

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.

Many thanks,
Francesco

4

Thanks @f.asnicar for the explanation! Yeah, it might be best to clarify a bit in the CLI docs.