only argparse

[soulios]

Changes in the utils.py for parsing all args correctly with cli overriding json.
Added options in the options.py
and remoced redundant code from main.py

[bernt-matthias]

One more request from my side. In the Galaxy wrappers we can distinguish a label and help text. My idea would be to use the first sentence of the argument help as label and the rest as help.

I made some suggestions (you can just use them in a commit .. can show you how if needed). Could you do this for the other classes or should be do it together?

[bernt-matthias]

Finally found some time to work on this. Sorry for the delay. With the renaming of the variables the automatic conversion of the argument parser to a Galaxy tool finally works.

Will continue now to add some tests and try to get it working (i.e. functional Galaxy tests).

For now I have one comment/question.

[bernt-matthias]

Currently the definition of the defaults is redundant. They are defined in the data classes and here. Would it be possible to pass an instance of the dataclasses to these functions and reuse the defaults?

For instance, for type you would need Options.

[bernt-matthias]

But I'm not sure if this interferes with the Galaxy tool generator, so it's more a question... Maybe we can test such a change for a single parameter first.