Code File Execution

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Code File Execution

Katherine Beaulieu
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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Re: Code File Execution

Peter Cock
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
<[hidden email]> wrote:

> Hi Everyone,
> Does anyone know how execution of code files happens? Is there a function
> somewhere that fills the parameters in?
> Cheers,
> Katherine
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: Code File Execution

Aysam Guerler
Hey Katherine,

It happens in basic.py. The code tag is executed to generate select options there. Look at:

Bye, Sam

On Mon, Nov 21, 2016 at 1:46 PM, Peter Cock <[hidden email]> 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
<[hidden email]> wrote:
> Hi Everyone,
> Does anyone know how execution of code files happens? Is there a function
> somewhere that fills the parameters in?
> Cheers,
> Katherine
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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