I would like to modify BBduk trimming and filtering parameters but don’t see those options. How do I change minavgquality, trimq and qtrim options?
Welcome, @vgaysin
Try expanding the Advanced Options section on the tool form to find all of the supported parameters.
Screenshot
Some tools have so many options! It helps to nest these a bit. If you expand all the sections on a form you’ll probably find everything that a scientist would be interested in tuning. If something seems to be missing, you can ask about it here and we’ll try to learn the reason, and potentially put in a request to the developers.
Please let us know if this helps! 
Update
Hi @vgaysin We discussed your question internally, and the options you want are not actually on this form. BBMerge can be used for some of this (sort of) but that would only apply filter before the kmer search, not after. This seems worth a request to the tool developers. I’ve done that here → Request: Consider including additional command line parameters on BBduk wrapped tool form · Issue #6448 · galaxyproject/tools-iuc · GitHub
If you would like to clarify with the use case or add in anything else, you can do that in this topic and the developers will see it, or you are welcome to post to the Github ticket directly. The original design was driven by an example, and while I don’t know if the current choices were due to resource management concerns or something else, this is how to find out.
Thanks for the request!