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having a directory and all contents retained as the 'output'

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having a directory and all contents retained as the 'output'

Brian Haas
Greetings,

I have a process that is going to generate dozens of output files,
each of which I want to retain as a data repository that will be
leveraged by other downstream tools.  I could just point the
downstream tool at the directory, and it'll know what to look for,
rather than to have to list each output file as a separate parameter.

Is it possible to do this in Galaxy?  And is there a best practice (or
example) for it?

thanks!

-b

--
--
Brian J. Haas
Manager, Genome Annotation and Analysis, Research and Development
The Broad Institute
http://broad.mit.edu/~bhaas
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Re: having a directory and all contents retained as the 'output'

Jeremy Goecks
Brian,

Composite datatypes are what you want:

<a href="http://wiki.g2.bx.psu.edu/Admin/Datatypes/Composite Datatypes">http://wiki.g2.bx.psu.edu/Admin/Datatypes/Composite%20Datatypes

Tool that use composite datatypes include the rGenetics tools and velvetg:

/tools/rgenetics/
tools/sr_assembly/velvetg

Best,
J.

On Jul 26, 2012, at 8:22 AM, Brian Haas wrote:

Greetings,

I have a process that is going to generate dozens of output files,
each of which I want to retain as a data repository that will be
leveraged by other downstream tools.  I could just point the
downstream tool at the directory, and it'll know what to look for,
rather than to have to list each output file as a separate parameter.

Is it possible to do this in Galaxy?  And is there a best practice (or
example) for it?

thanks!

-b

--
--
Brian J. Haas
Manager, Genome Annotation and Analysis, Research and Development
The Broad Institute
http://broad.mit.edu/~bhaas
___________________________________________________________
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/


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Re: having a directory and all contents retained as the 'output'

Brian Haas
Excellent!  Thanks!  I'll have a look,

-b

On Thu, Jul 26, 2012 at 10:45 AM, Jeremy Goecks <[hidden email]> wrote:

> Brian,
>
> Composite datatypes are what you want:
>
> http://wiki.g2.bx.psu.edu/Admin/Datatypes/Composite%20Datatypes
>
> Tool that use composite datatypes include the rGenetics tools and velvetg:
>
> /tools/rgenetics/
> tools/sr_assembly/velvetg
>
> Best,
> J.
>
> On Jul 26, 2012, at 8:22 AM, Brian Haas wrote:
>
> Greetings,
>
> I have a process that is going to generate dozens of output files,
> each of which I want to retain as a data repository that will be
> leveraged by other downstream tools.  I could just point the
> downstream tool at the directory, and it'll know what to look for,
> rather than to have to list each output file as a separate parameter.
>
> Is it possible to do this in Galaxy?  And is there a best practice (or
> example) for it?
>
> thanks!
>
> -b
>
> --
> --
> Brian J. Haas
> Manager, Genome Annotation and Analysis, Research and Development
> The Broad Institute
> http://broad.mit.edu/~bhaas
> ___________________________________________________________
> 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/
>
>



--
--
Brian J. Haas
Manager, Genome Annotation and Analysis, Research and Development
The Broad Institute
http://broad.mit.edu/~bhaas
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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