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/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)


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