[galaxy-dev] Possible to define a datatype corresponding to a directory?

[Ross]

Hi, Len.

Please take a look at
https://bitbucket.org/galaxy/galaxy-central/wiki/CompositeDatatypes and see
if that might help?

You can copy or create arbitrary files in the directory stored as the html
datatype's extra_files_path.
To make them visible and accessible to the user, write a list of href links
in a valid html page of the html datatype - the display automagically deals
with looking in the extra_files_path to find them.

Composite objects are also great for organizing messing tool outputs for
display and might be what you are looking for to pass bunches of files to
tools. Note that since your tools will need to look in the html file's
extra_files_path, that needs to be passed in to your tools on the command
line.

Hope this helps get you going.


Fri, Oct 22, 2010 at 8:21 PM, Len Trigg <len at realtimegenomics.com> wrote:

> Hi all,
>
> I have just downloaded galaxy, got up and running with a local
> installation. I'd like to have a crack at integrating some of our tools into
> the system.
>
> To start off with, we use a data format that is actually a directory
> containing multiple (variable number of) files and subdirectories. Is it
> possible to define a datatype that treats this directory as a single object
> in terms of using it as tool inputs and outputs?
>
> It seems like I could define a datatype corresponding to a zipped version
> of the directory (and this would be useful for uploading), but once it's
> uploaded I don't want the tools to be packing and unpacking zipfiles all the
> time.
>
>
> Cheers,
> Len.
>
> _______________________________________________
> galaxy-dev mailing list
> galaxy-dev at lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>



-- 
Ross Lazarus MBBS MPH
Associate Professor, Harvard Medical School
Director of Bioinformatics, Channing Laboratory
181 Longwood Ave., Boston MA 02115, USA.
Tel: +1 617 505 4850
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