Command tag in Galaxy

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Command tag in Galaxy

Sumedha Ganjoo
Hi,

I have been trying to do nested if-else and use logical operators to decide the executable to be called and the
parameters passed to it, in a tool xml file. Is it possible to do so in Galaxy tool files? How?
I have been getting errors in parsing the nested if-else.

Thanks in advance.

Regards,
Sumedha


--
Sumedha Ganjoo
Graduate Assistant,
Department Of Computer Science,
University Of Georgia,
Athens, GA , USA

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Re: Command tag in Galaxy

Jesse Erdmann
Hi,

Galaxy uses Cheetah templating in various parts of the XML file
including the <command> tag.  For a full description of Cheetah go to
http://www.cheetahtemplate.org/.

Here's an example from Galaxy's bitbucket wiki
(http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax):

<command interpreter="python">
    #if $source.source_select=="database" #blat_wrapper.py 0
$source.dbkey $input_query $output1 $iden $tile_size $one_off
    #else #blat_wrapper.py 1 $source.input_target $input_query
$output1 $iden $tile_size $one_off
    #end if
</command>

Regards,
Jesse Erdmann

On Tue, Jun 29, 2010 at 3:02 PM, Sumedha Ganjoo <[hidden email]> wrote:

> Hi,
>
> I have been trying to do nested if-else and use logical operators to decide
> the executable to be called and the
> parameters passed to it, in a tool xml file. Is it possible to do so in
> Galaxy tool files? How?
> I have been getting errors in parsing the nested if-else.
>
> Thanks in advance.
>
> Regards,
> Sumedha
>
>
> --
> Sumedha Ganjoo
> Graduate Assistant,
> Department Of Computer Science,
> University Of Georgia,
> Athens, GA , USA
>
> _______________________________________________
> galaxy-dev mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
>



--
Jesse Erdmann
Bioinformatics Analyst
Masonic Cancer Center
University of Minnesota
[hidden email]
612-626-3123

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Twitter: http://twitter.com/jesseerdmann
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