Hey Katherine, It happens in basic.py. The code tag is executed to generate select options there. Look at: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/parameters... Bye, Sam On Mon, Nov 21, 2016 at 1:46 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

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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