I am working on a project to automate workflow generation and its execution and I found the XML tool config schema kind of interesting, in order to properly specify a tool interface. However, if I understand it right, the idea of the XML tool config is to provide a description of the galaxy graphical user interface rather then a general description of the actual tool's interface. So I started to write an XSLT to transform the galaxy tool config to another xml, which I believe, better fits my needs.

In order to achieve this, I have a few questions:

- param tag: I havent really understood how you define a parameter to be mandatory or optional. I see when it is the child of the repeat element that there is (maybe) a minimum defined. But when this is not the case, how can I conclude that the parameter is optional vs. mandatory ?

- param tag's help attribute: can I assume any format, or is it simply the output of the tools help command ?

- when do you update the tools and in turn the XML configs. (e.g. the gatk stuff is kind of outdated: 1.4 vs 2.6 )