On Tue, Oct 26, 2010 at 12:51 PM, Len Trigg <len@realtimegenomics.com> wrote:

Ross wrote:

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.

OK, that looks like it might do the trick. Do you know if it supports directories being placed in the extra_files_path?

Never tried, but I'm going to guess that's possible. Any thoughts, Dan?

You'll need to take care of it in terms of tools that try to use the data and writing the links so the display works - let us know how you go?

(The "Composite Datasets" section of http://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput seems to imply that the additional content can only be files, not directories)

I think it's probably written that way because the code to generate the index for an 'auto_primary_file' composite object was designed to create a single level index of files - it could probably be made to create links for a recursive walk of the entire tree if that were ever needed - but I think you could use a 'basic' composite object and create your own complex index ?

Cheers,
Len.

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@realtimegenomics.com <mailto:len@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.

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