As I was running some diversity analyses, I noticed that the plugin includes a --cmd-config option, yet I could not much information on what parameters can be passed through this file, and how the file should be formatted. Thank you in advance for the help!
Hi @Sirtaj-Singh! Good eye - cmd-config is an undocumented option in q2cli. It is a supported flag in all plugins, on all Methods and Visualizers.
I am unsure if it will remain a feature of the cli interface in the future - it provides a lot of the same functionality as a generic shell script. For now, if it is something you are interested in playing with a bit more, this might get you started: