XML wrapper : use cheetath variable in from_work_dir tag

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XML wrapper : use cheetath variable in from_work_dir tag

Laure QUINTRIC
Hello,

I don't know how to use a cheetah variable (#set var) inside a XML tag.
I mean when I try to do this :


#set foo = "file.txt"
...
<outputs>
        <data format="txt" from_work_dir="something/${foo}" name="test"/>
</outputs>

from_work_dir tag contains "something/${foo}" instead of
"something/file.txt"

Is there a way to do this ?

Regards
Laure
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Re: XML wrapper : use cheetath variable in from_work_dir tag

John Chilton
There is not a way to do this. The exact value of from_work_dir needs
to be known prior to evaluating the cheetah environment. If you need
to variably define the output location - my recommendation would be to
just drop form the from_work_dir attribute and append  "; cp
something/${foo} $test" to the end of your command - this copy has to
be done either way so I don't think this is any less efficient. Let me
know if this doesn't make sense and good luck!

-John

On Wed, Jan 22, 2014 at 2:37 AM, lquintri <[hidden email]> wrote:

> Hello,
>
> I don't know how to use a cheetah variable (#set var) inside a XML tag.
> I mean when I try to do this :
>
>
> #set foo = "file.txt"
> ...
> <outputs>
>         <data format="txt" from_work_dir="something/${foo}" name="test"/>
> </outputs>
>
> from_work_dir tag contains "something/${foo}" instead of
> "something/file.txt"
>
> Is there a way to do this ?
>
> Regards
> Laure
> ___________________________________________________________
> 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:
>  http://lists.bx.psu.edu/
>
> 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/