I've been tweaking the blast+ tool xml to simplify database selection for our 
users (we have a lot of databases) and have made it multi-tiered through the 
use of two select boxen and a filter.
Basically, I've added an extra column to blastdb.loc with a group name, then 
use this as a filter to only display the group of databases that were chosen in 
the top select. 
Surprisingly it works - but I doubt it was the intention of the devs who wrote 
the filter code!

But there's a small bug that I can't see, the selects work correctly but I get 
a warning on the secondary one "An invalid option was selected, please verify"
Any ideas what I've overlooked?

Ideally I'd like to only read the file once and load into a data structure then 
populate the second select based on the choice from the top one - but that may 
be asking too much from Cheetah and Galaxy?

Thanx,

--Russell


My select code looks like this:

    <param name="db_type_select" type="select"  label="Subject database type">
        <options from_file="blastdb.loc.4col">
           <column name="value" index="3"/>
           <column name="name" index="3"/>
       <filter type="unique_value" name="name"  column="3"  />
       <filter type="sort_by" name="name"  column="3"  />
      </options>
    </param>

    <param name="species_select" type="select"  label="Database name">
        <options from_file="blastdb.loc.4col">
            <column name="value" index="0"/>
            <column name="name" index="1"/>
            <column name="path" index="2"/>
        <filter type="param_value" ref="db_type_select" column="3"/>
      </options>
    </param>


This is an example of the extra column added to blastdb.loc:

agall.seq       All AgResearch ESTs     
/dataset/blastdata/active/species/agall.seq     AgR Databases
agruminant_plus.seq     All AgResearch Ruminant ESTs, plus NCBI public Bos 
Taurus as at 3/2002, plus NCBI Sheep at 7/2002       
/dataset/blastdata/active/species/agruminant_plus.seq  Ruminant Databases
galaxy-dev@inconstant$ head -n20 ../../tool-data/blastdb.loc.4col
arrayprinturg15k.seq    15Kurg (ESTs)   
/dataset/blastdata/active/species/arrayprinturg15k.seq  Microarray Databases
454AllContigs.fna       454 Seqs 20/5/2007   
/dataset/blastdata/active/species/454AllContigs.fna     Sheep Databases
AffyBovineArray052006.seq       Affy Bovine Array at 5/2006     
/dataset/blastdata/active/species/AffyBovineArray052006.seq     Cattle Databases
AFT_Affy_chip_seqs.fa   AFT Affy Array 6/2006   
/dataset/blastdata/active/species/AFT_Affy_chip_seqs.fa Fungal Databases
agilent_mouse   Agilent Mouse Array 012694 (as at 2/2007)       
/dataset/blastdata/active/species/agilent_mouse Rodent Databases
est     all public ESTs         /dataset/blastdata/active/species/est   Pub 
Databases
est_others      all "other" public ESTs (other than Human Databases, mouse)     
/dataset/blastdata/active/species/est_others    Pub Databases
agall_plus.seq  All AgResearch ESTs, plus NCBI public Bos Taurus as at 3/2002, 
plus NCBI Sheep at 7/2002        
/dataset/blastdata/active/species/agall_plus.seq      AgR Databases
agall.seq       All AgResearch ESTs     
/dataset/blastdata/active/species/agall.seq     AgR Databases
agruminant_plus.seq     All AgResearch Ruminant ESTs, plus NCBI public Bos 
Taurus as at 3/2002, plus NCBI Sheep at 7/2002       
/dataset/blastdata/active/species/agruminant_plus.seq  Ruminant Databases
agruminant.seq  All AgResearch Ruminant ESTs    
/dataset/blastdata/active/species/agruminant.seq        Ruminant Databases
build2_allssr.seq       All BT2.0 SSRs  
/dataset/blastdata/active/species/build2_allssr.seq     Cattle Databases
Allium_cepa     Allium cepa DFCI gene indices   
/dataset/blastdata/active/species/Allium_cepa   Plant Databases
angrep.ref      angrep.ref      /dataset/blastdata/active/species/angrep.ref    
Repeat Databases
fungalnucs_AR3018_454   AR3018 454 reads, trimmed, 12/2009      
/dataset/blastdata/active/species/fungalnucs_AR3018_454 Fungal Databases
fungalnucs_AR3018_454ContigsNewbler2.0  AR3018 454 build, 12/2009       
/dataset/blastdata/active/species/fungalnucs_AR3018_454ContigsNewbler2.0        
Fungal Databases


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