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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