I have been looking into re-using the galaxy toolconfig xml files outside galaxy, for auto-generating wizards for command line tools, in an own little (eclipse based) software (For a short background, see [1]).

I have come to realize though that the xml-files are not really independent, but (almost?) always is accompanied by a correpsonding .py file, which does more or less tricks, which seemingly makes it very hard to use the xml-files outside a galaxy/python environment at all.

My questions:
1. Are the xml-files *always* accompanied by the .py file, or is that optional?
2. Would my idea be possible/reasonable at all?
3. Are there other more general tool config formats that I could use, since I'm not using galaxy atm?
4. Any other suggestions or ideas?

Best Regards
// Samuel

[1]: The tool is built as a complement to some galaxy initiatives at the UPPMAX HPC Center in Uppsala. Specifically we need a light-weight way to configure batch scripts for the software installed at UPPMAX, of which bioinformatics tools are just a part. The galaxy toolconfig xml-format looked useful though, and seemed to enable us to have at least most of our bioinformatics tools (the category with most installed tools at UPPMAX) already configured.

System Expert / Bioinformatician
SNIC-UPPMAX / SciLifeLab Uppsala
Uppsala University, Sweden
E-mail: samuel.la...@scilifelab.uu.se
Phone: +46 (0)18 - 471 1060
WWW: http://www.uppmax.uu.se
Uppnex: https://www.uppnex.uu.se

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