Hi Peter,
I don't understand how a sub-class would work here - an example would be great.
See GFF and GTF for an example of how subclassing datatypes works; also, the BED classes in lib/galaxy/datatypes/interval.py use subclasses as well. Typically, additional metadata and functionality is provided in the subclass.
In addition to the type of sequence in FASTA (DNA, RNA, or protein) it struck me that the variant of FASTQ file (Sanger, Solexa, Illumina 1.3+) would also be a situation which might benefit from file sub-types in Galaxy.
Perhaps. Because there are so many types of FASTA files, careful thought is needed about how to organize the many FASTA types so that they are useful both to users and to Galaxy. It might be good to come up with an idea of how things would work and post back to galaxy-dev to get some feedback before implementation. J.