Are you asking how Galaxy takes the user-entered parameters
(requested in the tool XML file with <input> tags) and builds a
command line string using the Cheetah-format template defined
in the <command> tag?

At least part of the answer to that is the ToolEvaluator object:

https://github.com/galaxyproject/galaxy/blob/71cea6604d43c5fe6215f5656462ba6c1af69bb6/lib/galaxy/tools/evaluation.py#L454

Peter

On Mon, Nov 21, 2016 at 6:37 PM, Katherine Beaulieu
<katherine.beaulieu014@gmail.com> wrote:
> Hi Everyone,
> Does anyone know how execution of code files happens? Is there a function
> somewhere that fills the parameters in?
> Cheers,
> Katherine
>

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