User-friendly CLI

[c089]

To avoid confusing users we should improve the way command line arguments are parsed. At least it should:

• show usage information when invoked without arguments, or with -h or --help
• show a helpful error message if any of the arguments are missing or of the wrong type

If this becomes too cumbersome to implement with the very simple minimist engine, it might be good consider using a full-featured parsing engine such as yargs for this.

[yochannah]

Apologies for completely poking my nose in out of the blue - I was browsing tickets, saw this one and thought this might be of interest since it's relevant... https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-2-15
"Ten recommendations for creating usable bioinformatics command line software"

:) hope the link is of some use!!