Re: [galaxy-dev] Managing large database lists in tool wrappers?

31 Mar 2014

      Those macros look great and are exactly what I want :-)

Thanx,

--Russell

-----Original Message-----
From: Björn Grüning [mailto:bjoern.gruening@gmail.com] 
Sent: Tuesday, 1 April 2014 11:07 a.m.
To: Smithies, Russell; Björn Grüning; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Managing large database lists in tool wrappers?

Hi Russell,

Am 31.03.2014 23:46, schrieb Smithies, Russell:
...
Hi Bjoern,
Yes I'm aware of the macros but I've never managed to get them to work 
;-(
Lets try to get them to work. It will do exactly what you want.
The Homer Tools should be a easy enough to get you started:

https://github.com/bgruening/galaxytools/tree/master/homer/tools
...
What I'd like is something like a php include tag to pull the contents of a whole file into another file so I'm not repeating myself eg. for the database lists in the megablast, blastn, and tblastn wrappers.
Those select fields are nice, and in "ordinary" html and JQuery you 
can do grouping but as far as I can tell it's not possible with Galaxy/Cheetah XML templating - though we are a few versions behind so may have overlooked recent updates.
Not yet, but I think it would be easy to implement it. It's used in other areas of Galaxy a lot.

Ciao,
Bjoern
...
Thanx for your suggestions,
--Russell
-----Original Message-----
From: galaxy-dev-bounces@lists.bx.psu.edu 
[mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Björn 
Grüning
Sent: Tuesday, 1 April 2014 10:19 a.m.
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Managing large database lists in tool wrappers?
Hi Russell,
would something like a http://ivaynberg.github.io/select2/ field work for you?
What do you mean with <include> tags? Are you aware of Galaxy macros?
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Direct_XML
_Macros
Cheers,
Bjoern
Am 31.03.2014 22:58, schrieb Smithies, Russell:
...
Does anyone have a workable solution to managing and displaying large lists in tool wrappers?
eg.  a database list containing hundreds of enteries in the blast+ tool? (we have 1,056 different blast databases).
As a work-around we've split our blast databases into species (eg cow, sheep, fungus, clover, fish, rice, etc)  then faked a multi-select to pull in those sub-database files with conditional selectors like this:
<conditional name="db_opts">
          <param name="db_opts_selector" type="select" label="Nucleotide Database Type">
            <option value="pub" selected="True">Pub Databases</option>
            <option value="cattle">Cattle Databases</option>
            <option value="sheep">Sheep Databases</option>
            <option value="deer">Deer Databases</option>
            <option value="ruminant">Ruminant Databases</option>
            <option value="dog">Dog Databases</option>
            <option value="fungi">Fungi Databases</option>
            <option value="invertebrates">Invertebrates Databases</option>
            <option value="microarrays">Microarrays Databases</option>
            <option value="marsupials">Marsupials Databases</option>
            <option value="rodent">Rodent Databases</option>
            <option value="viruses">Viruses Databases</option>
            <option value="human">Human Databases</option>
            <option value="microarrays">Microarrays Databases</option>
              </param>
<when value="ruminant">
                  <param name="database" type="select" label="Ruminant Nucleotide BLAST database" help="">
                      <options from_file="blastdb.ruminant.loc">
                        <column name="value" index="0"/>
                        <column name="name" index="1"/>
                        <column name="path" index="2"/>
                      </options>
                  </param>
                  <param name="subject" type="hidden" value="" />
              </when>
<when value="misc">
                  <param name="database" type="select" label="Misc Nucleotide BLAST database" help="">
                      <options from_file="blastdb.misc.loc">
                        <column name="value" index="0"/>
                        <column name="name" index="1"/>
                        <column name="path" index="2"/>
                      </options>
                  </param>
                  <param name="subject" type="hidden" value="" />
              </when>
We end up with a lot of duplication between tool wrappers (I've never managed to get an <include> tag working)  and these aren't exactly simple to maintain so does anyone have a better solution?
I had thought about tacking an extra field onto the .loc files with a "species" and doing some grouping with that but haven't progressed that idea very far yet.
Any suggestions greatly appreciated :)
Thanx,
--Russell
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