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

31 Mar 2014

      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

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

Smithies, Russell