#-------------------------- blastall  ( 6/28/04) ----------------------
# The environment variable $BLASTDB should be set to the location
# of database files formated by formatdb.

item:BLASTALL - sequence database search
itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta;nice -n 10 blastall -i in1.fasta -p $PROGRAM -d $DBASE -M $MATRIX -Q $GENCODE  -D $GENCODE -S $STRANDS -g $GAPPED -e $EVALUE -m $VOPTIONS  > in1.$PROGRAM; nedit in1.$PROGRAM; python $BIRCH/script/dbsout.py in1.$PROGRAM $WHERE; rm in1*) &
itemhelp: doc/blast/blastall.help.txt

in:in1
informat:flat
insave:

arg:PROGRAM
arglabel:PROGRAM
argtype:choice_menu
argchoice:blastp - protein vs. protein database:blastp
argchoice:blastn - DNA vs. DNA database:blastn
argchoice:blastx - translated DNA vs. protein database:blastx
argchoice:tblastn - protein vs. translated DNA database:tblastn
argchoice:blastx - translated DNA vs. translated DNA database:tblastx
argvalue:0


arg:DBASE
argtype:choice_menu
arglabel:Database
argchoice:SwissProt:swissprot
argchoice:GenBank NonRedundant (Protein):nr
argchoice:GenBank NonRedundant:nt
argchoice:GenBank Plant pln_nt:pln_nt
argchoice:GenBank Mamalian mam_nt:mam_nt
argchoice:GenBank Human EST:est_human
argchoice:GenBank Mouse EST:est_mouse
argchoice:GenBank Other EST:est_others
argchoice:GenBank Vector:vector
argchoice:GenBank STS:sts
agrvalue:0

arg:STRANDS
arglabel:Strands to search
argtype:chooser
argchoice:both:3
argchoice:top:1
argchoice:bottom:2
argvalue:0

arg:GAPPED
arglabel:Perform gapped alignment?
argtype:chooser
argchoice:Yes:T
argchoice:No:F
argvalue:0

arg:MATRIX
arglabel:SCORING MATRIX
argtype:choice_menu
argchoice:Blosum45 (Protein):BLOSUM45
argchoice:Blosum62 (Protein default):BLOSUM62
argchoice:Blosum80 (Protein):BLOSUM80
argchoice:PAM30 (Protein):PAM30
argchoice:PAM70 (Protein):PAM70
argvalue:1

arg:GENCODE
argtype:choice_menu
arglabel:Genetic Code
argchoice:Standard:1
argchoice:Vertebrate Mitochondrial:2
argchoice:Yeast Mitochondrial:3
argchoice:Mold, Protozoan, and Coelenterate Mitochondrial:4
argchoice:Invertebrate Mitochondrial:5
argchoice:Ciliate, Dasycladacean and Hexamita:6
argchoice:Echinoderm and Flatworm:9
argchoice:Euplotid:10
argchoice:Bacterial and Plant Plastid:11
argchoice:Alternative Yeast Nuclear:12
argchoice:Ascidian Mitochondrial:13
argchoice:Alternative Flatworm Mitochondrial:14
argchoice:Blepharisma:15
argchoice:Chlorophycean Mitochondrial:16
argchoice:Trematode Mitochondrial:21
argchoice:Scenedesmus obliquus mitochondrial:22
argchoice:Thraustochytrium Mitochondrial:23
argvalue:0

arg:EVALUE
argtype:choice_menu
arglabel:# matches expected by random chance
argchoice:1.0e-11:1.0e-11
argchoice:1.0e-10:1.0e-10
argchoice:1.0e-9:1.0e-9
argchoice:1.0e-8:1.0e-8
argchoice:1.0e-7:1.0e-7
argchoice:1.0e-6:1.0e-6
argchoice:1.0e-5:1.0e-5
argchoice:0.0001:0.0001
argchoice:0.001:0.001
argchoice:0.01:0.01
argchoice:0.1:0.1
argchoice:1:1
argchoice:10:10
argchoice:100:100
argvalue:9

arg:VOPTIONS
argtype:choice_menu
arglabel:Alignment view options
argchoice:pairwise:0
argchoice:query-anchored showing identities:1
argchoice:query-anchored no identities:2
argchoice:flat query-anchored, show identities:3
argchoice:flat query-anchored, no identities:4
argchoice:query-anchored no identities and blunt ends:5
argchoice:flat query-anchored, no identities and blunt ends:6
argchoice:XML Blast output:7
argchoice:tabular:8
argchoice:tabular with comment lines:9
argchoice:ASN, text:10 -J 
argvalue:0

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Textedit windows:-d textedit
argchoice:Output file:-d files $OUTNAME
argvalue:0

arg:OUTNAME
arglabel:Output file name
argtype:text