Hi all,

we are planning to work on a project to implement a Galaxy fuse based
shell. Probably starting with the work from Clare [1].

Next to our Galaxy IPython integration it should attract
more bioinformaticians and should offer a new way to interact with
Galaxy. This includes moving, deleting datasets, but also executing
tools and workflows. For the latter I would like to have some sort of
bash auto-completion. Type in your tool/workflow and you will see all
the parameters you can/should modify, in addition to your normal help page.

Currently the parameter identifiers (<param name="foo">) do not need to
be meaningful. In fact many tools invent their own unique names, to
identify a parameter in the cheetah section. This name is always unique
but it's hard to guess it's meaning from just the name and are also not
mappable to the original parameter name. This makes tool execution from
the API sometimes hard.

I would like to propose a new attribute for all <param> tags. This
should specify a unique value that 100% matches the original parameter
name of the underlying tool.

This attribute could be used to:
 * automatically enhance the help text of each parameter. Currently best
practise it to include this parameter in brackets at the end of each
help text. We can do this now automatically, or only show it by mouse
over etc ...
 * In a Galaxy shell, the user could just type in a normal command (-i
history1/foo.bam -o history1/bar.sam) and Galaxy shell would be able
to map this parameter to the correct <param> tag in Galaxy

I greatly appreciate any comments!

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