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 <h...@fmi.ch
<mailto:h...@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)
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