It would help if you could point to an existing tool that works the way you want. I don't know of any that deal with arbitrary nested directories containing arbitrary files. A new composite datatype could impose a structure that a tool could be written to deal with (eg the pbed datatype used in some rgenetics tools) but arbitrary data structures are not going to be possible AFAIK. You're unlikely to get useful help without a much more complete and clear explanation of the problem.

On Thu, Jan 3, 2013 at 1:50 PM, <> wrote:
Hi Ross,
             I think I need to clarify. I have a file in /home/galaxy/data-test/dir1/dir2/somefile.txt

Under the "Upload files from filesystem paths", In the "path to upload" window I paste "/home/galaxy/data-test". This then puts the "somefile.txt" in the /home/galaxy/galaxy-dist/database/files/000 directory. However, I elected to keep the directory structure. I can see this if I navigate through the "shared data" tab but where is this information stored under the galaxt-dist structure. As my application needs to have the directory structure kept, so need to access it from the xml/command line

I thought it might have been something like: /home/galaxy/galaxy-dist/database/files/000/data-test/dir1/dir2/dataset_id.dat. But this is not the case rather  /home/galaxy/galaxy-dist/database/files/000/dataset_id.dat. i.e. no directory structure. So how can I access this information from the xml files in the tools directory?

From: Ross []
Sent: Wednesday, January 02, 2013 4:43 PM
To: Burdett, Neil (ICT Centre, Herston - RBWH)
Cc: galaxy-user
Subject: Re: [galaxy-user] Upload files from filesystem paths

Try importing those library files to the history where you want them - browse the Galaxy 'shared data' tab to where you uploaded them.

On Wed, Jan 2, 2013 at 11:39 AM, <<>> wrote:
   I have a local galaxy installation.

I've created a data library, selected "Upload files from filesystem paths", pasted a path in the "path to upload" window, and I've selected to preserve the directory structure". And the files get imported.

How do I now access these files from my application? I don't want to import them into the history as then they lose the directory structure. I can't see where they are physically under the galaxy-dist structure

Thanks for any help