menu:File

item:test cmask output
itemmethod: textedit in1

in:in1
informat:colormask

item:New sequence   <meta N>
itemmethod:echo "$Type$Name" > out1
itemmeta:n
itemhelp:new_sequence.help
 
arg:Name 
argtype:text 
arglabel:New Sequence name? 
argtext:New 
 
arg:Type 
argtype:choice_list 
arglabel:Type? 
argchoice:DNA/RNA:# 
argchoice:Amino Acid:% 
argchoice:Text:\"
argchoice:Mask:@ 

out:out1
outformat:flat

item:Import Foreign Format
itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp
itemhelp:readseq.help

arg:INPUTFILE
argtype:text
arglabel:Name of foreign file?

out:OUTPUTFILE
outformat:genbank

item:Export Foreign Format
itemmethod:readseq INPUTFILE -a -f$FORMAT > $OUTPUTFILE
itemhelp:readseq.help

arg:FORMAT
argtype:choice_list
argchoice:IG/Stanford:1
argchoice:GenBank:2
argchoice:NBRF:3
argchoice:EMBL:4
argchoice:GCG:5
argchoice:DNA Strider:6
argchoice:Fitch:7
argchoice:Pearson:8
argchoice:Zuker:9
argchoice:Olsen:10
argchoice:Phylip v3.2:11
argchoice:Phylip v3.3:12
argchoice:Plain text:13

arg:OUTPUTFILE
argtype:text
arglabel:Save as?

in:INPUTFILE
informat:genbank


item:Save Selection
itemmethod: cat $SAVE_FUNC > $Name
itemhelp:save_selection.help

arg:SAVE_FUNC
argtype:chooser
arglabel:File format
argchoice:Flat:in1
argchoice:Genbank:in2
argchoice:GDE/HGL:in3

arg:Name
argtype:text
arglabel:File name?

in:in1
informat:flat

in:in2
informat:genbank

in:in3
informat:gde

item:Print Selection
itemmethod:(PrintStrat in1 $SCALE > in1.tmp; $CMD -P$PRINTER in1.tmp; /bin/rm -f in1 in1.tmp)&
itemhelp:print_alignment.help
 
arg:SCALE
argtype:slider
arglabel:Reduce printout by?
argmin:1
argmax:20
argvalue:1

arg:CMD
argtype:chooser
argchoice:Lpr:lpr
argchoice:Enscript Gaudy:enscript -G -q
argchoice:Enscript Two column:enscript -2rG
 
arg:PRINTER
argtype:text
arglabel:Which printer?
argtext:lp
 
in:in1
informat:gde
insave:

menu:Edit

item:Sort
itemmethod:(heapsortHGL in1 $PRIM_KEY $SEC_KEY > in1.tmp ; gde in1.tmp;/bin/rm -f in1*)&
itemhelp:heapsortHGL.help

arg:PRIM_KEY
argtype:choice_list
argchoice:Group:group-ID
argchoice:type:type
argchoice:name:name
argchoice:Sequence ID:sequence-ID
argchoice:creator:creator
argchoice:offset:offset
arglabel:Primary sort field?

arg:SEC_KEY
argtype:choice_list
argchoice:None:
argchoice:Group:group-ID
argchoice:type:type
argchoice:name:name
argchoice:Sequence ID:sequence-ID
argchoice:creator:creator
argchoice:offset:offset
arglabel:Secondary sort field?

in:in1
informat:gde
insave:

item:extract
itemmethod:(gde in1;/bin/rm -f in1)&

in:in1
informat:gde
inmask:
insave:

menu:DNA/RNA

item:Translate...
itemmethod:Translate -tbl $TBL -frame $FRAME -min_frame $MNFRM $LTRCODE in1 > out1

arg:FRAME
argtype:chooser
arglabel:Which reading frame?
argchoice:First:1
argchoice:Second:2
argchoice:Third:3
argchoice:All six:6

arg:MNFRM
arglabel:Minimum length of AA sequence to translate?
argtype:slider
argmin:0
argmax:100
argvalue:20

arg:LTRCODE
argtype:chooser
arglabel:Translate to:
argchoice:Single letter codes:
argchoice:Triple letter codes:-3

arg:TBL
arglabel:Codon table?
argtype:chooser
argchoice:universal:1
argchoice:mycoplasma:2
argchoice:yeast:3
argchoice:Vert. mito.:4
in:in1
informat:gde

out:out1
outformat:gde

item:Dot plot
itemmethod:(DotPlotTool in1 ; /bin/rm -f in1)&
itemhelp:DotPlotTool.help

in:in1
informat:gde
insave:

item:Clustal alignment
itemmethod:(tr '%#' '>'<in1>clus_in;clustalw -quicktree -output=PIR -infile=clus_in -align  > in1.rpt;sed "s/>DL;/#/g" < clus_in.pir> in1;$REPORT gde in1;/bin/rm -f clus_in* in1*   )&

itemhelp:clustal_help

arg:KTUP
argtype:slider
arglabel:K-tuple size for pairwise search
argmin:1
argmax:10
argvalue:2

arg:WIN
argtype:slider
arglabel:Window size
argmin:1
argmax:10
argvalue:4

arg:Trans
argtype:chooser
arglabel:Transitions weighted?
argchoice:Yes:/TRANSIT
argchoice:No:

arg:FIXED
argtype:slider
arglabel:Fixed gap penalty
argmin:1
argmax:100
argvalue:10

arg:FLOAT
arglabel:Floating gap penalty
argtype:slider
argmin:1
argmax:100
argvalue:10

arg:REPORT
argtype:chooser
arglabel:View assembly report?
argchoice:No:
argchoice:Yes:textedit in1.rpt&

 
in:in1
informat:flat
insave:

item:Variable Positions
itemmethod:varpos $REV < in1 > out1

arg:REV
argtype:chooser
arglabel:Highlight (darken)
argchoice:Conserved positions:
argchoice:variable positions:-rev

in:in1
informat:flat

out:out1
outformat:colormask

item:Phrap
itemmethod:readseq in1 -a -f8 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp; phrap OUTPUTFILE; readseq -a -f2 OUTPUTFILE.contigs > out1;/bin/rm -rf OUTPUT*;

in:in1
informat:genbank

out:out1
outformat:genbank



item:Find all <meta-f>
itemmethod:findall $SEARCH $PRCNT $CASE $UT -match $MAT -mismatch $MIS < in1 > out1;
itemhelp:findall.help 
itemmeta:f
 
arg:SEARCH
argtype:text
arglabel:Search String
 
arg:PRCNT
argtype:slider
arglabel:Percent mismatch
argmin:0
argmax:75
argvalue:10
 
arg:CASE
argtype:chooser
arglabel:Case
argchoice:Upper equals lower:
argchoice:Upper not equal lower:-case
 
arg:UT
argtype:chooser
arglabel:U equal T?
argchoice:Yes:-u=t
argchoice:No:
argvalue:0
 
arg:MAT
arglabel:Match color
argtype:choice_list
argchoice:yellow:1
argchoice:violet:2
argchoice:red:3
argchoice:aqua:4
argchoice:green:5
argchoice:blue:6
argchoice:grey:11
argchoice:black:8
argvalue:2
 
arg:MIS
argtype:choice_list
arglabel:Mismatch color
argchoice:yellow:1
argchoice:violet:2
argchoice:red:3
argchoice:aqua:4
argchoice:green:5
argchoice:blue:6
argchoice:grey:11
argchoice:black:8
argvalue:7

in:in1
informat:flat
 
out:out1
outformat:colormask

item:Sequence Consensus
itemmethod:(MakeCons in1 $METHOD $MASK > out1)
itemhelp:MakeCons.help

arg:METHOD
arglabel:Method
argtype:chooser
argchoice:IUPAC:-iupac
argchoice:Majority:-majority $PERCENT

arg:MASK
argtype:chooser
arglabel:Create a new:
argchoice:Sequence:
argchoice:Selection Mask: | Consto01mask

arg:PERCENT
arglabel:Minimum Percentage for Majority
argtype:slider
argmin:50
argmax:100
argvalue:75

in:in1
informat:gde

out:out1
outformat:gde


item:MFOLD
itemmethod:(tr 'a-z' 'A-Z' < seqGB > .GDE.tmp.caps; ZUKERGDE.sh .GDE.tmp.caps $CT $GDE_HELP_DIR/ZUKER/ > out1 && $METHOD < out1; Zuk_to_gen < $CT >file.gen; gde file.gen& textedit RegionTable; /bin/rm -f RegionTable out1 seqGB* .GDE.tmp.caps)&
itemhelp:MFOLD.help

in:seqGB
informat:genbank
insave:

arg:METHOD
argtype:chooser
arglabel:RNA type
argchoice:Fold Linear RNA:lrna
argchoice:Fold Circular RNA:crna

arg:CT
argtype:text
arglabel:Pairing(ct)  File Name
argtext:mfold_out


item:Draw Secondary structure
itemmethod:(LoopTool $TEMPLATE in1 ; /bin/rm -f in1) &
itemhelp:LoopTool.help

arg:TEMPLATE
argtype:chooser
arglabel:Use template file ./loop.temp?
argchoice:No:
argchoice:Yes:-t loop.temp

in:in1
informat:genbank
insave:

item:Highlight helix
itemmethod:readseq -a -f8 in1 | sed "s/>HELIX/\"HELIX/" > in1.flat; sho_helix < in1.flat > out1;rm in1.flat
itemhelp:sho_helix.help

in:in1
informat:genbank

out:out1
outformat:colormask


#Menu for DNA/RNA

item:blastn
itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; /usr/local/biotools/blast/blastall -p blastn -d $BLASTDB -i in1.f -W $WORDLEN -M $MATCH  > in1.tmp; /usr/openwin/bin/textedit in1.tmp; rm in1*)&

in:in1
informat:flat
insave:

arg:BLASTDB
argtype:choice_list
arglabel:Which Database
argchoice:Genome HIV position:/var/www/cgi-bin/db/genomeHIV.fasta
argchoice:genbank update:$GDE_HELP_DIR/BLAST/genupdate
argchoice:HIV-1:/var/www/cgi-bin/db/hivallsequencesGB-31-10.fasta
argchoice:HIV-1 Subtype:/var/www/cgi-bin/db/subcomplete.fasta
argchoice:HIV-1 HXB2 Numb:/var/www/cgi-bin/db/HXB2.fasta
argchoice:HIV-1 HXB2 Numb:/var/www/cgi-bin/db/HXB2.fasta
arg:WORDLEN
argtype:slider
arglabel:Word Size
argmin:4
argmax:18
argvalue:12

arg:MATCH
argtype:slider
arglabel:Match Score
argmin:1
argmax:10
argvalue:5

arg:MMSCORE
argtype:slider
arglabel:Mismatch Score
argmin:-10
argmax:-1
argvalue:-5

item:blastx
itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blastx $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE> in1.tmp; textedit in1.tmp; rm in1* PAM???)&

in:in1
informat:flat
insave:

arg:BLASTDB
argtype:choice_list
arglabel:Which Database
argchoice:pir1:$GDE_HELP_DIR/BLAST/pir
argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept

arg:WORDLEN
argtype:slider
arglabel:Word Size
argmin:1
argmax:5
argvalue:3

arg:Matrix
arglabel:Substitution Matrix:
argtype:choice_list
argchoice:PAM120:PAM120
argchoice:PAM250:PAM250

arg:CODE
argtype:choice_list
arglabel:Genetic Code
argchoice:Standard or Universal:0
argchoice:Vertebrate Mitochondrial:1
argchoice:Yeast Mitochondrial:2
argchoice:Mold Mitochondrial and Mycoplasma:3
argchoice:Invertebrate Mitochondrial:4
argchoice:Ciliate Macronuclear:5
argchoice:Protozoan Mitochondrial:6
argchoice:Plant Mitochondrial:7
argchoice:Echinodermate Mitochondrial:8


item:FASTA (DNA/RNA)
itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; textedit in1.out;\rm in1*) &
itemhelp:FASTA.help

in:in1
informat:flat

arg:DBASE
argtype:choice_list
arglabel:Database
argchoice:GenBank Primate:$GDE_HELP_DIR/FASTA/GENBANK/gbpri.seq\ 1
argchoice:GenBank Rodent:$GDE_HELP_DIR/FASTA/GENBANK/gbrod.seq\ 1
argchoice:GenBank all Mammal:$GDE_HELP_DIR/FASTA/GENBANK/gbmam.seq\ 1
argchoice:GenBank verteBrates:$GDE_HELP_DIR/FASTA/GENBANK/gbvrt.seq\ 1
argchoice:GenBank Inverts:$GDE_HELP_DIR/FASTA/GENBANK/gbinv.seq\ 1
argchoice:GenBank pLants:$GDE_HELP_DIR/FASTA/GENBANK/gbpln.seq\ 1
argchoice:GenBank Struct RNA:$GDE_HELP_DIR/FASTA/GENBANK/gbrna.seq\ 1
argchoice:GenBank euk. Organelles:$GDE_HELP_DIR/FASTA/GENBANK/gborg.seq\ 1
argchoice:GenBank phaGe:$GDE_HELP_DIR/FASTA/GENBANK/gbphg.seq\ 1
argchoice:GenBank bacTeria:$GDE_HELP_DIR/FASTA/GENBANK/gbbct.seq\ 1
argchoice:GenBank sYnthetic:$GDE_HELP_DIR/FASTA/GENBANK/gbsyn.seq\ 1
argchoice:GenBank Viral:$GDE_HELP_DIR/FASTA/GENBANK/gbvrl.seq\ 1
argchoice:GenBank Unannotated:$GDE_HELP_DIR/FASTA/GENBANK/gbuna.seq\ 1

arg:NUMOFALN
argtype:slider
arglabel:Number of Alignment to Report
argmin:1
argmax:100
argvalue:20

arg:MATRIX
arglabel:Which SMATRIX
argtype:choice_list
argchoice:Default:
argchoice:altdiag.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/altdiag.mat
argchoice:altprot.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/altprot.mat
argchoice:dna.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/dna.mat
argchoice:prot.mat:-s $GDE_HELP_DIR/FASTA/MATRIX/prot.mat

menu:DB
item:DB X8873
itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp
itemhelp:readseq.help

arg:INPUTFILE
argtype:chooser
arglabel:Databases
argchoice:subtype:/home/database/DNA/subtyperef/subcomplete.fasta 
argchoice:SIVENVDNA.fasta:/home/database/DNA/SIVENVDNA.fasta

out:OUTPUTFILE
outformat:genbank

item:HIV-1 Subtype
itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp
itemhelp:readseq.help

arg:INPUTFILE
argtype:choice_list
arglabel:HIV-1 Subtype genome regions
argchoice:CG:/home/database/DNA/subtyperef/subcomplete.fasta 
argchoice:sub5ltr.fasta:/home/database/DNA/subtyperef/sub5ltr.fasta
argchoice:sub5ltrU3.fasta:/home/database/DNA/subtyperef/sub5ltrU3.fasta
argchoice:sub5ltrU5.fasta:/home/database/DNA/subtyperef/sub5ltrU5.fasta
argchoice:subenv.fasta:/home/database/DNA/subtyperef/subenv.fasta
argchoice:subenv-gp120.fasta:/home/database/DNA/subtyperef/subenv-gp120.fasta
argchoice:subenv-gp41.fasta:/home/database/DNA/subtyperef/subenv-gp41.fasta
argchoice:subenvv3.fasta:/home/database/DNA/subtyperef/subenvv3.fasta
argchoice:subgag.fasta:/home/database/DNA/subtyperef/subgag.fasta
argchoice:subgag-p17.fasta:/home/database/DNA/subtyperef/subgag-p17.fasta
argchoice:subgag-p24.fasta:/home/database/DNA/subtyperef/subgag-p24.fasta
argchoice:subgag-pol.fasta:/home/database/DNA/subtyperef/subgag-pol.fasta
argchoice:subpol.fasta:/home/database/DNA/subtyperef/subpol.fasta
argchoice:subpol-p15RNAase.fasta:/home/database/DNA/subtyperef/subpol-p15RNAase.fasta
argchoice:subpol-p31integrase.fasta:/home/database/DNA/subtyperef/subpol-p31integrase.fasta
argchoice:subpol-p51RT.fasta:/home/database/DNA/subtyperef/subpol-p51RT.fasta
argchoice:subpol-protease.fasta:/home/database/DNA/subtyperef/subpol-protease.fasta
argchoice:subrevCDS.fasta:/home/database/DNA/subtyperef/subrevCDS.fasta
argchoice:subrevexon1.fasta:/home/database/DNA/subtyperef/subrevexon1.fasta
argchoice:subrevexon2.fasta:/home/database/DNA/subtyperef/subrevexon2.fasta
argchoice:subrevintron.fasta:/home/database/DNA/subtyperef/subrevintron.fasta
argchoice:subTAR.fasta:/home/database/DNA/subtyperef/subTAR.fasta
argchoice:subtatCDS.fasta:/home/database/DNA/subtyperef/subtatCDS.fasta
argchoice:subtatexon1.fasta:/home/database/DNA/subtyperef/subtatexon1.fasta
argchoice:subtatexon2.fasta:/home/database/DNA/subtyperef/subtatexon2.fasta
argchoice:subtatintron.fasta:/home/database/DNA/subtyperef/subtatintron.fasta
argchoice:subvif.fasta:/home/database/DNA/subtyperef/subvif.fasta
argchoice:subvpr.fasta:/home/database/DNA/subtyperef/subvpr.fasta
argchoice:subvpu.fasta:/home/database/DNA/subtyperef/subvpu.fasta
argchoice:subnef.fasta:/home/database/DNA/subtyperef/subnef.fasta
out:OUTPUTFILE
outformat:genbank



item:HXB2
itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp
itemhelp:readseq.help

arg:INPUTFILE
argtype:chooser
arglabel:HXB2 Reference Seq
argchoice:CG:/home/database/DNA/HXB2.fasta

out:OUTPUTFILE
outformat:genbank

menu:Protein

item:Clustal Protein Alignment
itemmethod:(tr '%#"' '>' <in1>clus_in;clustalw /output=PIR /infile=clus_in /align /ktup=$KTUP /window=$WIN $Matrx  /fixedgap=$FIXED /floatgap=$FLOAT > in1.rpt;sed "s/>P1;/%/g" < clus_in.pir > in1;$REPORT gde in1;/bin/rm -f in1* clus_in* gde* )&
itemhelp:clustal_help

arg:KTUP
argtype:slider
arglabel:K-tuple size for pairwise search
argmin:1
argmax:10
argvalue:2

arg:WIN
argtype:slider
arglabel:Window size
argmin:1
argmax:10
argvalue:4

arg:Matrx
argtype:chooser
arglabel:Weighting matrix
argchoice:PAM 250:PAM250
argchoice:PAM 100:PAM100
argchoice:Identity:ID

arg:FIXED
argtype:slider
arglabel:Fixed gap penalty
argmin:1
argmax:100
argvalue:10
 
arg:FLOAT
arglabel:Floating gap penalty
argtype:slider
argmin:1
argmax:100
argvalue:10

arg:REPORT
argtype:chooser
arglabel:View assembly report?
argchoice:No:
argchoice:Yes:textedit in1.rpt&
 
in:in1
informat:flat
insave:

#Menu for Protein

item:blastp
itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blastp $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;textedit in1.tmp; rm in1* PAM???)&

in:in1
informat:flat
insave:

arg:BLASTDB
argtype:choice_list
arglabel:Which Database
argchoice:pir:$GDE_HELP_DIR/BLAST/pir
argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept
argchoice:local:$GDE_HELP_DIR/BLAST/local_db

arg:Matrix
arglabel:Substitution Matrix:
argtype:choice_list
argchoice:PAM120:PAM120
argchoice:PAM250:PAM250

arg:WORDLEN
argtype:slider
arglabel:Word Size
argmin:1
argmax:5
argvalue:3

item:tblastn
itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; tblastn $BLASTDB in1.f W=$WORDLEN M=$Matrix C=$CODE > in1.tmp; textedit in1.tmp; rm in1* PAM???)&

in:in1
informat:flat
insave:

arg:BLASTDB
argtype:choice_list
arglabel:Which Database
argchoice:genbank:$GDE_HELP_DIR/BLAST/genbank
argchoice:genbank update:$GDE_HELP_DIR/BLAST/genupdate

arg:Matrix
arglabel:Substitution Matrix:
argtype:choice_list
argchoice:PAM120:PAM120
argchoice:PAM250:PAM250

arg:WORDLEN
argtype:slider
arglabel:Word Size
argmin:4
argmax:18
argvalue:12

arg:CODE
argtype:choice_list
arglabel:Genetic Code
argchoice:Standard or Universal:0
argchoice:Vertebrate Mitochondrial:1
argchoice:Yeast Mitochondrial:2
argchoice:Mold Mitochondrial and Mycoplasma:3
argchoice:Invertebrate Mitochondrial:4
argchoice:Ciliate Macronuclear:5
argchoice:Protozoan Mitochondrial:6
argchoice:Plant Mitochondrial:7
argchoice:Echinodermate Mitochondrial:8

item:blast3
itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp $GDE_HELP_DIR/BLAST/PAM??? .; blast3 $BLASTDB in1.f W=$WORDLEN M=$Matrix > in1.tmp;textedit in1.tmp; rm in1* PAM???)&

in:in1
informat:flat
insave:

arg:BLASTDB
argtype:choice_list
arglabel:Which Database
argchoice:pir1:$GDE_HELP_DIR/BLAST/pir
argchoice:genpept:$GDE_HELP_DIR/BLAST/genpept

arg:Matrix
arglabel:Substitution Matrix:
argtype:choice_list
argchoice:PAM120:PAM120
argchoice:PAM250:PAM250

arg:WORDLEN
argtype:slider
arglabel:Word Size
argmin:1
argmax:5
argvalue:3

item:FASTA (Protein)
itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta;fasta -Q -d $NUMOFALN $MATRIX in1.fasta $DBASE > in1.out; textedit in1.out;\rm in1*) &
itemhelp:FASTA.help

in:in1
informat:flat

arg:DBASE
argtype:choice_list
arglabel:Database
argchoice:NBRF PIR1:$GDE_HELP_DIR/FASTA/PIR/pir1.dat\ 2
argchoice:NBRF PIR2:$GDE_HELP_DIR/FASTA/PIR/pir2.dat\ 2
argchoice:NBRF PIR3:$GDE_HELP_DIR/FASTA/PIR/pir3.dat\ 2


arg:NUMOFALN
argtype:slider
arglabel:Number of Alignment to Report
argmin:1
argmax:100
argvalue:20

arg:MATRIX
arglabel:Which SMATRIX
argtype:choice_list
argchoice:Default:
argchoice:Minimum mutation matrix:-s $GDE_HELP_DIR/FASTA/MATRIX/codaa.mat
argchoice:Identity matrix:-s $GDE_HELP_DIR/FASTA/MATRIX/idnaa.mat
argchoice:Identity matrix for mismatches:-s $GDE_HELP_DIR/FASTA/MATRIX/idpaa.mat
argchoice:PAM250:-s $GDE_HELP_DIR/FASTA/MATRIX/pam250.mat
argchoice:PAM120:-s $GDE_HELP_DIR/FASTA/MATRIX/pam120.mat

menu:Seq management

item:Assemble Contigs
itemmethod:(sed "s/#/>/"<in1 >in1.tmp; CAP2 in1.tmp $OVERLAP $PMATCH > out1;/bin/rm -f in1.tmp)
itemhelp:CAP2.help

arg:OVERLAP
argtype:slider
arglabel:Minimum overlap?
argmin:5
argmax:100
argvalue:20

arg:PMATCH
argtype:slider
arglabel:Percent match required within overlap
argmin:25
argmax:100
argvalue:90

in:in1
informat:flat

out:out1
outformat:gde
outoverwrite:

item:Map View
itemmethod:(mapview in1 -pbl $PBL -npp $NPP; /bin/rm -f in1)&
itemhelp:mapview.help

in:in1
informat:gde
insave:

arg:PBL
arglabel:Pixel Between Lines
argtype:slider
argvalue:10
argmin:1
argmax:15

arg:NPP
arglabel:Nucleotides Per Pixel
argtype:slider
argvalue:1
argmin:1
argmax:20

arg:LWIDTH
arglabel:Line Thickness
argtype:slider
argvalue:2
argmin:1
argmax:5


item:Restriction sites
itemmethod:(cp $ENZ in1.tmp ; $PRE_EDIT Restriction in1.tmp in1 > out1 ; rm in1.tmp);
itemhelp:Restriction.help

arg:ENZ
argtype:text
arglabel:Enzyme file
argtext:$GDE_HELP_DIR/DATA_FILES/enzymes

arg:PRE_EDIT
argtype:chooser
arglabel:Edit enzyme file first?
argchoice:Yes:textedit in1.tmp;
argchoice:No: 

in:in1
informat:flat

out:out1
outformat:colormask

menu:Phylogeny

item:DeSoete Tree fit
itemmethod: (readseq -a -f8 in1>in1.flat;count -t $CORR in1.flat> in1.tmp ; lsadt<in1.tmp -seed $SEED -init $INIT -empty -99.9 > in1.out ; $DISPLAY_FUNC in1.out;/bin/rm -f in1* )&
itemhelp:lsadt.help

in:in1
informat:genbank
insave:
inmask:

arg:CORR
arglabel:Distance correction?
argtype:chooser
argchoice:Olsen:-c=olsen
argchoice:Jukes/Cantor:-c=jukes
argchoice:None:-c=none

arg:INIT
arglabel:Initial parameter estimate
argtype:choice_list
argchoice:uniformly distributed random numbers:1
argchoice:error-perturbed data:2
argchoice:original distance data from input matrix:3

arg:SEED
argtype:slider
arglabel:Random number seed
argmin:0
argmax:65535
argvalue:12345
 
arg:DISPLAY_FUNC
argtype:chooser
arglabel:View tree using
argchoice:TextEdit:textedit
argchoice:Treetool:treetool < 

item:Phylip help
itemmethod:(textedit $GDE_HELP_DIR/PHYLIP/$FILE)&

arg:FILE
argtype:choice_list
arglabel:Which program?
argchoice:boot:boot.doc
argchoice:clique:clique.doc
argchoice:consense:consense.doc
argchoice:contchar:contchar.doc
argchoice:contml:contml.doc
argchoice:contrast:contrast.doc
argchoice:discrete:discrete.doc
argchoice:distance:distance.doc
argchoice:dnaboot:dnaboot.doc
argchoice:dnacomp:dnacomp.doc
argchoice:dnadist:dnadist.doc
argchoice:dnainvar:dnainvar.doc
argchoice:dnaml:dnaml.doc
argchoice:dnamlk:dnamlk.doc
argchoice:dnamove:dnamove.doc
argchoice:dnapars:dnapars.doc
argchoice:dnapenny:dnapenny.doc
argchoice:dolboot:dolboot.doc
argchoice:dollop:dollop.doc
argchoice:dolmove:dolmove.doc
argchoice:dolpenny:dolpenny.doc
argchoice:draw:draw.doc
argchoice:drawgram:drawgram.doc
argchoice:drawtree:drawtree.doc
argchoice:factor:factor.doc
argchoice:fitch:fitch.doc
argchoice:gendist:gendist.doc
argchoice:kitsch:kitsch.doc
argchoice:main:main.doc
argchoice:mix:mix.doc
argchoice:move:move.doc
argchoice:neighbor:neighbor.doc
argchoice:penny:penny.doc
argchoice:protpars:protpars.doc
argchoice:read.me.general:read.me.general.doc
argchoice:restml:restml.doc
argchoice:seqboot:seqboot.doc
argchoice:sequence:sequence.doc


item:Phylip 3.4
itemmethod:(rm -f outfile ; readseq -a -f12 in1 | sed "s/ YF//1" > infile;$PREEDIT shelltool $PROGRAM;textedit outfile;rm in1 )&
 
arg:PROGRAM
argtype:choice_list
arglabel:Which program to run?
argchoice:DNAPARS:dnapars
argchoice:DNABOOT:dnaboot
argchoice:DNAPENNY:dnapenny
argchoice:DNAML:dnaml
argchoice:DNAMLK:dnamlk
argchoice:DNACOMP:dnacomp
argchoice:DNAMOVE:dnamove
argchoice:DNAINVAR:dnainvar
argchoice:PROTPARS:protpars

arg:PREEDIT
argtype:chooser
arglabel:Edit input before running?
argchoice:No:
argchoice:Yes:textedit infile;
 
in:in1
informat:genbank
inmask:
insave:
 
item:Phylip Distance methods
itemmethod:(readseq -a -f12 in1 | sed "s/ YF//1" > infile ; $PREEDIT shelltool seqboot; mv -f outfile infile; shelltool dnadist;mv -f outfile infile; shelltool neighbor; cp outtree intree; $PROGRAM  textedit outfile;/bin/rm -f in1 infile outfile)&
 
arg:PROGRAM
arglabel:Which method?
argtype:chooser
argchoice:DNADIST:mv -f infile outfile;
argchoice:Fitch:shelltool fitch;
argchoice:Kitsch:shelltool kitsch;
argchoice:Neighbor:shelltool neighbor;
argchoice:Full:shelltool consense;


arg:PREEDIT
argtype:chooser
arglabel:Edit input before running?
argchoice:No:
argchoice:Yes:textedit infile;
 
in:in1
informat:genbank
inmask:
insave:

menu:W
item:Stanford
itemmethod:(readseq in1 -a -f8 > infile.fasta; netscape http://hiv-4.stanford.edu/cgi-bin/hivseqweb.pl?uploaded_file=infile.fasta)&
in:in1
informat:genbank
item:Los Alamos DB Search
itemmethod:(netscape http://hiv-web.lanl.gov/cgi-bin/hivDB3/public/wdb/ssampublic)&
item:Retroviruses NCBI
itemmethod:(netscape http://www.ncbi.nlm.nih.gov/retroviruses/)&
item:SNAP (sy/nosy)&
itemmethod:(netscape http://hiv-web.lanl.gov/SNAP/WEBSNAP/SNAP.html)& 
item:PubMed
itemmethod:(netscape http://www.ncbi.nlm.nih.gov/Entrez/)


in:in1
informat:genbank




menu:Email

item:BLASTN
itemmethod:(echo BLASTPROGRAM blastn > in1.tmp; echo DATALIB $DBASE >> in1.tmp; echo MATCH $MSCORE >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail BLAST@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) &

arg:DBASE
argtype:choice_list
arglabel:Which Database?
argchoice:GenBank Qtrly & Updates:GenBank
argchoice:EMBL:embl

arg:MSCORE
argtype:slider
arglabel:Match Score
argmin:3
argmax:7
argvalue:5

in:in1
informat:flat
insave:

item:BLASTP
itemmethod:(echo BLASTPROGRAM blastp >in1.tmp; echo DATALIB $DBASE >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail BLAST@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) &

arg:DBASE
argtype:choice_list
arglabel:Which Database?
argchoice:Swiss-Prot:swiss-prot
argchoice:PIR:pir

in:in1
informat:flat
insave:

item:Fasta-(DNA)
itemmethod:(echo DATALIB $DBASE > in1.tmp; echo KTUP $KPL >> in1.tmp; echo SCORES $TOP >> in1.tmp; echo ALIGNMENTS $ALNG >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp;Mail SEARCH@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) &

arg:DBASE
argtype:choice_list
arglabel:Which GenBank Database?
argchoice:Qrtly & Updates:GenBank/all
argchoice:Updates:GenBank/new
argchoice:Primate:GenBank/primate
argchoice:Rodent:GenBank/rodent
argchoice:Other-Mammalian:GenBank/other_mammalian
argchoice:Other-Vertebrate:GenBank/other_vertebrate
argchoice:Invertebrate:GenBank/invertebrate
argchoice:Plant:GenBank/plant
argchoice:Organelle:GenBank/organelle
argchoice:Bacterial:GenBank/bacterial
argchoice:Structural-RNA:GenBank/structural_rna
argchoice:Viral:GenBank/viral
argchoice:Phage:GenBank/phage
argchoice:Synthetic:GenBank/synthetic
argchoice:Unannotated:GenBank/unannotated

arg:KPL
argtype:slider
arglabel:K-tuple window
argmin:3
argmax:6
argvalue:4

arg:TOP
argtype:slider
arglabel:Scores Displayed?
argmin:1
argmax:200
argvalue:100

arg:ALNG
argtype:slider
arglabel:# Alignments Displayed?
argmin:1
argmax:200
argvalue:20

in:in1
informat:flat
insave:

item:Fasta-(PROTEIN)
itemmethod:(echo DATALIB $DBASE > in1.tmp; echo KTUP $TPL >> in1.tmp; echo SCORES $SCRS >> in1.tmp; echo ALIGNMENTS $ALNMNTS >> in1.tmp; echo BEGIN >> in1.tmp; sed "s/-//g" < in1 | tr '@%#$' '>' >> in1.tmp; Mail SEARCH@GENBANK.BIO.NET < in1.tmp; rm in1 in1.tmp) &

arg:DBASE
argtype:choice_list
arglabel:Which Protein Database?
argchoice:Trans GenBank Qrtly:GenPept/all
argchoice:Trans GenBank Daily:GenPept/new
argchoice:Swiss-Protein:SWISS-PROT/all

arg:TPL
argtype:slider
arglabel:K-TUP window
argmin:1
argmax:2
argvalue:1

arg:SCRS
argtype:slider
arglabel:# Scores Displayed?
argmin:1
argmax:200
argvalue:100

arg:ALNMNTS
argtype:slider
arglabel:# Alignments Displayed?
argmin:1
argmax:200
argvalue:20

in:in1
informat:flat
insave:

item:GeneID
itemmethod:($REPRINT > in1.tmp; echo Genomic Sequence >> in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail geneid@darwin.bu.edu < in1.tmp; rm in1 in1.tmp) &

arg:REPRINT
argtype:chooser
arglabel:Do you want a GENEID reprint?
argchoice:YES:echo "Preprint Request" >> in1.tmp
argchoice:NO

in:in1
informat:flat
insave:

item:Sequence Retrieval
itemmethod:(echo $REGEXP > in1.tmp; Mail RETRIEVE@GENBANK.BIO.NET < in1.tmp; rm in1.tmp) &

arg:REGEXP
argtype:text
arglabel:Accession # or LOCUS name of sequence to retrieve

item:Grail
itemmethod:(echo Sequences $TOTALSEQS $ID > in1.tmp; sed "s/-//g" < in1 | tr '@%#' '>' >> in1.tmp; Mail grail@ornl.gov <in1.tmp; rm in1 in1.tmp) &

arg:REGISTER
argtype:chooser
arglabel:Have you previously registered for Grail services?
argchoice:YES
argchoice:NO:echo "YOU MUST REGISTER"

arg:TOTALSEQS
argtype:text
arglabel:Number of Sequences Being Sent to Grail?

arg:ID
argtype:text
arglabel:User ID (MUST HAVE PREVIOUSLY REGISTERED)

in:in1
informat:flat
insave:

item:Grail Registration
itemmethod:(echo Register > in1.tmp; echo $NAME >> in1.tmp; echo $ADDRESS >> in1.tmp; echo $PHONE >> in1.tmp; echo $EMAIL >> in1.tmp; Mail grail@ornl.gov < in1.tmp; rm in1.tmp)

arg:NAME
argtype:text
arglabel:Your Name

arg:ADDRESS
argtype:text
arglabel:Your Address

arg:PHONE
argtype:text
arglabel:Your Phone Number

arg:EMAIL
argtype:text
arglabel:Your E-Mail Address


#
# dgg added new readseq formats, 29 dec 92
#

item:Export Foreign Format
itemmethod:readseq in1 -pipe -all -form=$FORMAT > $OUTPUTFILE
itemhelp:readseq.help

arg:FORMAT
argtype:choice_list
argchoice:GenBank:genbank
argchoice:IG/Stanford:ig
argchoice:NBRF:nbrf
argchoice:EMBL:embl
argchoice:GCG:gcg
argchoice:DNA Strider:strider
argchoice:Fitch:fitch
argchoice:Pearson/Fasta:pearson
argchoice:Zuker:zuker
argchoice:Olsen:olsen
argchoice:Phylip:phylip
#argchoice:Phylip v3.2:phylip3.2
argchoice:Plain text:raw
argchoice:ASN.1:asn
argchoice:PIR:pir
argchoice:MSF:msf
argchoice:PAUP:paup
argchoice:Pretty:pretty -nametop -nameleft=3 -numright -nameright -numtop

arg:OUTPUTFILE
argtype:text
arglabel:Save as?

in:in1
informat:genbank


#
#dgg addition for new readseq, 24 dec 92
#

item:Pretty Print
itemmethod:readseq in1 -p -a -f=pretty $NAMELEFT $NAMERIGHT $NUMTOP $NUMBOT $NUMLEFT $NUMRIGHT -col=$COLS -width=$WIDTH $MATCH $GAPC > in1.pretty; (textedit in1.pretty; /bin/rm -f in1 in1.pretty)&
itemhelp:readseq.help

#nametop is bad !?

in:in1
informat:genbank

arg:NAMETOP
argtype:chooser
arglabel:Names at top  ?
argchoice:No:
argchoice:Yes:-nametop

arg:NAMELEFT
argtype:chooser
arglabel:Names at left ?
argchoice:No:
argchoice:Yes:-nameleft

arg:NAMERIGHT
argtype:chooser
arglabel:Names at right?
argchoice:Yes:-nameright
argchoice:No:

arg:NUMTOP
argtype:chooser
arglabel:Numbers at top  ?
argchoice:Yes:-numtop
argchoice:No:

arg:NUMBOT
argtype:chooser
arglabel:Numbers at tail ?
argchoice:No:
argchoice:Yes:-numbot

arg:NUMLEFT
argtype:chooser
arglabel:Numbers at left ?
argchoice:Yes:-numleft
argchoice:No:

arg:NUMRIGHT
argtype:chooser
arglabel:Numbers at right?
argchoice:Yes:-numright
argchoice:No:

arg:MATCH
argtype:chooser
arglabel:Use match '.' for 2..n species?
argchoice:No:
argchoice:Yes:-match

arg:GAPC
argtype:chooser
arglabel:Count gap symbols?
argchoice:No:
argchoice:Yes:-gap

arg:WIDTH
argtype:slider
arglabel:Sequence width?
argmin:10
argmax:200
argvalue:50

arg:COLS
argtype:slider
arglabel:Column spacers?
argmin:0
argmax:50
argvalue:10


### pretty print insert end
#

item:Wally's test function
itemmethod:run__wally $ONE $TWO $THREE < $FILE

arg:ONE
argtype:chooser
arglabel:How?
argchoice:Fast:-fast
argchoice:Slow:-slow

arg:TWO
argtype:slider
argmin:0
argmax:100
argvalue:50
arglabel:how many?

arg:THREE
argtype:choice_list
arglabel:Which one?
argchoice:Fast:-fast
argchoice:Slow:-slow

arg:FILE
argtype:text
arglabel:Which file