possible improvements

[bernt-matthias]

Here some possible improvements (for now I have a solution for all of them):

• remove spaces in tool name (problem comes for subcommands)
• <command interpreter="python"><!\[CDATA\[ -> <command><!\[CDATA\[python
• non optional positional arguments are currently treated as optional in the galaxy xml file
• Is it possible to use the name of positional arguments instead of naming them positional_NUMBER? If there are multiple positionals with the same name one could still number them.

This would simplify automated postprocessing quite a bit.

Example: checkm outliers -h

positional arguments:
out_folder folder specified during qa command
bin_folder folder containing bins (fasta format)
tetra_profile tetranucleotide profiles for each sequence (see tetra command)
output_file print results to file

Are now positional1,..., positional 4

I would like to use sed/grep to replace the corresponding parts of the xml with appropriate content.

[hexylena]

I'd love to see all of this!

I'm afraid I've got a couple of other higher priority things for approximately the next month, so if you want most of this, I'd be happy to review any pull requests you make. Sorry I don't have more time for this repository.