Re: [galaxy-dev] Send repeat parameter to code file for multiple select list
On Thu, Sep 1, 2016 at 9:36 AM, Katherine Beaulieu < katherine.beaulieu014@gmail.com> wrote:
Hi Peter, The code file tag is generally used in populating select lists. So basically you have a function from a code file that is loaded before runtime of the tool and you can dynamically load content based on that function and you can pass it parameters from your tool but I'm wondering how you would pass it the contents of a repeat parameter. This is how the code file tag works: https://wiki.galaxyproject.org/Admin/Tools/Custom%20Code Thanks, Katherine
On Thu, Sep 1, 2016 at 8:23 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
I'm not quite sure what you mean by a "code file", but if you mean using the <configfile> tag, here's an example:
https://github.com/peterjc/galaxy_mira/blob/master/tools/mir a4_0/mira4_de_novo.xml
I am using a Cheetah syntax for loop to access each entry in a repeat parameter.
Peter
On Thu, Sep 1, 2016 at 12:58 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Hello Galaxy Community, I was wondering if anyone had ever come across a situation where they have had to pass the contents of a repeat parameter to a code file in a Galaxy tool config? Is there any way to do this? Katherine
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Ah - I understand what you mean now. Using the code tag is discouraged, but you may find some of these examples useful for what you are trying to do: https://github.com/galaxyproject/galaxy/issues/2714 I hope that helps, Peter On Thu, Sep 1, 2016 at 2:37 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
On Thu, Sep 1, 2016 at 9:36 AM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Hi Peter, The code file tag is generally used in populating select lists. So basically you have a function from a code file that is loaded before runtime of the tool and you can dynamically load content based on that function and you can pass it parameters from your tool but I'm wondering how you would pass it the contents of a repeat parameter. This is how the code file tag works: https://wiki.galaxyproject.org/Admin/Tools/Custom%20Code Thanks, Katherine
On Thu, Sep 1, 2016 at 8:23 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
I'm not quite sure what you mean by a "code file", but if you mean using the <configfile> tag, here's an example:
https://github.com/peterjc/galaxy_mira/blob/master/tools/mira4_0/mira4_de_no...
I am using a Cheetah syntax for loop to access each entry in a repeat parameter.
Peter
On Thu, Sep 1, 2016 at 12:58 PM, Katherine Beaulieu <katherine.beaulieu014@gmail.com> wrote:
Hello Galaxy Community, I was wondering if anyone had ever come across a situation where they have had to pass the contents of a repeat parameter to a code file in a Galaxy tool config? Is there any way to do this? 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/
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___________________________________________________________ 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/
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participants (2)
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Katherine Beaulieu -
Peter Cock