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stuff is kind of outdated: 1.4 vs 2.6 )

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