add galaxy support #249
Description
pyqi currently has support for optparse and HTML interfaces. It would be awesome to also have some sort of support for a galaxy interface.
@josenavas has existing code to convert old-style QIIME scripts to galaxy configuration files. This code may make sense to add to pyqi.
I'm thinking that we could have a new (command-line) pyqi command, something like:
pyqi convert-galaxy -m pyqi.interfaces.optparse.config -o galaxy_conf_output
which would take a directory of pyqi optparse config files as input, and create a directory of galaxy configuration files as output.
Another approach is to make galaxy a full-fledged interface of its own, where it would have its own type of config files (i.e., like optparse and HTML interface). We'd still need a command to load these conf files and create the equivalent galaxy XML files.
I'm leaning towards the first approach since galaxy is just wrapping command-line tools, and I think it will have all the info it needs in the optparse config files to do the conversion. If we go this route, it also means less duplicated code/configuration since we won't have to add separate galaxy config files for each command.
If we end up needing more info that is galaxy-specific (and can't shoehorn it into the optparse config structure), the second option would make more sense.
@josenavas @wasade @ebolyen @gregcaporaso thoughts?