Hi Nik Have a look at the "Profile Annotations" tool (~/tools/annotation_profiler/annotation_profiler.xml) and the file ~/tool-data/annotation_profiler_options.xml Regards, Hans-Rudolf On 04/19/2014 12:48 AM, Nikhil Joshi wrote:

Hi Hans,

Thanks for your response. I am trying to get just one part working right now, and that is the selecting of a database file. You suggest using a drill_down, but I can't seem to find good documentation on how to get it to work. I have been looking at the annotation_profiler tool to get ideas, but it still is unclear to me. Can you give me a simple example of how one would create the file that the drill_down would use and then how to use that file?

- Nik.

On Wed, Apr 9, 2014 at 1:13 AM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>> wrote:

Hi Nik

I don't think there is a solution out of the box for all of this, but I will try to give you some pointers - others might have different or even better suggestions (my suggestion are very 'hacky'). Let me answer your questions in reverse order:

- Instead of using "Add another file", display all your files as checkboxes:

type="select" display="checkboxes" multiple="true"

you then get a comma separated string with containing all the selected files

one option to populate the checkboxes is using "dynamic_options" or "from_file" which both allow you to read the list of files stored in a extra table

- A list with thousands of files to choose from is obviously not very handy. You can build a tree where you can open and collapse individual branches using

type="drill_down" together with "from_file"

Or as an alternative to searching, you can use "conditional" and then only display part of the list.

- you can write a little tool, which allows people to select a history item (or uploads a new file) which is then stored at a new location (outside the galaxy database directory). In a second step, this tool adds the item to the table which is read by "dynamic_options" or "from_file". Using "from_file" would require a restart, but a tool reload.

I hope you get a few ideas out of this

Regards, Hans-Rudolf

On 04/09/2014 04:34 AM, Nikhil Joshi wrote:

Hi all,

We have a local install of Galaxy that we use for testing for our bioinformatics courses. I am creating some new tool interfaces for the install. I want to create a tool that will allow a user to automatically add a fasta database to the "built-in" databases (without needing to reboot the server). Is this possible?

Along with that issue is that the number of databases for this tool can number in the thousands. Is there a way to easily search the built-in databases for the database you are looking for, and then use that database in a tool? Right now, it is an enormous drop down list which is really annoying and unwieldy.

Finally, these tools can take multiple input files, but I really don't like the way galaxy handles that where you have to continually click on "Add another file". Is there a method or work-around in galaxy where you can have a multi-file select?

- Nik.

-- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.__edu/ <http://bioinformatics.ucdavis.edu/> najoshi -at- ucdavis -dot- edu 530.752.2698 <tel:530.752.2698> (w)

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-- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)