On Tue, Feb 7, 2012 at 9:52 PM, Beale, Holly (NIH/NHGRI) [F]
<holly.be...@nih.gov> wrote:
> Hi all --
> I'd like to know what programs are used when I run a tool on my data.
> Ideally I'd also like to know what parameters are passed to command
> line tools.

The short answer is you can't, other than by reading the tool's
documentation (ideally within Galaxy below the options), and/or
reading the tool's source code (the XML file plus any scripts).

Some Galaxy tools are simple wrappers for a single command
line tool, in which case it is usually clear how the parameters
offered to you in the Galaxy interface translate to matching
command line arguments. Such Galaxy tools should make
this clear in their documentation, along with giving you clear
citation information for the underlying tools.

Other Galaxy tools are complex scripts/tools that may call
several other command line tools internally

So it depends.

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