How about an optional argument for exact matching versus subclass matching?
Bonus points to follow the API style of Python string's .startwith(...) where in addition to a single prefix you can give a tuple, for instance .startswith(("Hello", "Hi")) e.g. $input1.is_of_type(('fastq', 'fasta'))
If you don't add optional arguments, then this might be nicer - variable number of arguments: $input1.is_of_type('fastq', 'fasta')
Note this can be done already with $input1.is_of_type('fastq') or $input1.is_of_type('fasta')
For exact matching I think I would just prefer people did $input.ext == 'fastq'. I wouldn't mind making $input1.is_of_type('fastq', 'fasta') work - but it makes my concern that the method name is not quite right grow. Hmmm... I'll update the pull request.