1menu: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:FASTA:8
argchoice:NEXUS:17
argchoice:Phylip v3.3:12
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:SNAP
itemmethod: cat in1 > infile;/usr/local/biotools/GDE/bin/fasta2snap.pl > outfile;  /usr/bin/X11/xterm -e  /home/tulio/biotools/SNAP/SNAP.pl outfile; textedit backg*; textedit summ*; sheeltool /home/tulio/biotools/codons-xyplot.pl codons.*; textedit codon.data; /bin/rm -rf back* codon* summ*;

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




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:codeml
itemmethod:(readseq -a -f11 in1 | sed "s/ YF//1" > test.phy;  /usr/bin/X11/xterm -e  codeml $METHOD)&


arg:METHOD
arglabel:Which method ?
argtype:chooser
argchoice:0:/home/tulio/biotools/paml/method0.ctl
argchoice:1:/home/tulio/biotools/paml/method1.ctl
argchoice:2:/home/tulio/biotools/paml/method2.ctl
argchoice:3:/home/tulio/biotools/paml/method3.ctl
argchoice:4:/home/tulio/biotools/paml/method4.ctl
argchoice:5:/home/tulio/biotools/paml/method5.ctl
argchoice:6:/home/tulio/biotools/paml/method6.ctl


in:in1
informat:genbank
inmask:
insave:

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:HIV-1 Seq. Db.:/var/www/cgi-bin/db/hiv17-08-01.fasta2
argchoice:HIV-1 Subtype:/var/www/cgi-bin/db/subcomplete.fasta
argchoice:HIV-1 HXB2 Numbering:/var/www/cgi-bin/db/HXB2.fasta
argchoice:HCV Numbering:/var/www/cgi-bin/db/HCV.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; /usr/local/biotools/blast/blastall -p blastx -d $BLASTDB -i in1.f -W $WORDLEN -M PAM30  > in1.tmp; /usr/openwin/bin/textedit in1.tmp; rm in1*)&



in:in1
informat:flat
insave:

arg:BLASTDB
argtype:choice_list
arglabel:Which Database
argchoice:HIV Proteins:/var/www/cgi-bin/db/hiv17-08-01.PROT.fasta
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:PAM30:PAM30
argchoice:PAM70:PAM70

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:HIV Seq. Db.
item:Ref. Seq. for Drug Resistance
itemmethod:cp $INPUTFILE OUTFILE.tmp;readseq OUTFILE.tmp -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp
itemhelp:readseq.help

arg:INPUTFILE
argtype:chooser
arglabel:Sequence
argchoice:Prot function:/database/AA/protease.mutations.fasta
argchoice:rt function:/database/AA/rtmutations.fasta
argchoice:pNL4-3 CG :/database/DR/pNL4-3.CG.fasta
argchoice:pNL4-3 protease :/database/DR/pNL4-3.prot$format.fasta
argchoice:pNL4-3 RT :/database/DR/pNL4-3.RT$format.fasta
argchoice:HXB2 CG :/database/DR/HXB2.fasta
argchoice:HXB2 protease :/database/DR/HXB2.prot$format.fasta
argchoice:HXB2 RT :/database/DR/HXB2.RT$format.fasta
argchoice:data1.fasta:/database/DNA/data1.fasta


arg:format
argtype:chooser
arglabel:Format
argchoice:DNA:
argchoice:AA:AA

out:OUTPUTFILE
outformat:genbank

item:HIV-1 Subtype Db.
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:/database/DNA/subtyperef/subcomplete.fasta 
argchoice:sub5ltr.fasta:/database/DNA/subtyperef/sub5ltr.fasta
argchoice:sub5ltrU3.fasta:/database/DNA/subtyperef/sub5ltrU3.fasta
argchoice:sub5ltrU5.fasta:/database/DNA/subtyperef/sub5ltrU5.fasta
argchoice:subenv.fasta:/database/DNA/subtyperef/subenv.fasta
argchoice:subenv-gp120.fasta:/database/DNA/subtyperef/subenv-gp120.fasta
argchoice:subenv-gp41.fasta:/database/DNA/subtyperef/subenv-gp41.fasta
argchoice:subenvv3.fasta:/database/DNA/subtyperef/subenvv3.fasta
argchoice:subgag.fasta:/database/DNA/subtyperef/subgag.fasta
argchoice:subgag-p17.fasta:/database/DNA/subtyperef/subgag-p17.fasta
argchoice:subgag-p24.fasta:/database/DNA/subtyperef/subgag-p24.fasta
argchoice:subgag-pol.fasta:/database/DNA/subtyperef/subgag-pol.fasta
argchoice:subpol.fasta:/database/DNA/subtyperef/subpol.fasta
argchoice:subpol-p15RNAase.fasta:/database/DNA/subtyperef/subpol-p15RNAase.fasta
argchoice:subpol-p31integrase.fasta:/database/DNA/subtyperef/subpol-p31integrase.fasta
argchoice:subpol-p51RT.fasta:/database/DNA/subtyperef/subpol-p51RT.fasta
argchoice:subpol-protease.fasta:/database/DNA/subtyperef/subpol-protease.fasta
argchoice:subrevCDS.fasta:/database/DNA/subtyperef/subrevCDS.fasta
argchoice:subrevexon1.fasta:/database/DNA/subtyperef/subrevexon1.fasta
argchoice:subrevexon2.fasta:/database/DNA/subtyperef/subrevexon2.fasta
argchoice:subrevintron.fasta:/database/DNA/subtyperef/subrevintron.fasta
argchoice:subTAR.fasta:/database/DNA/subtyperef/subTAR.fasta
argchoice:subtatCDS.fasta:/database/DNA/subtyperef/subtatCDS.fasta
argchoice:subtatexon1.fasta:/database/DNA/subtyperef/subtatexon1.fasta
argchoice:subtatexon2.fasta:/database/DNA/subtyperef/subtatexon2.fasta
argchoice:subtatintron.fasta:/database/DNA/subtyperef/subtatintron.fasta
argchoice:subvif.fasta:/database/DNA/subtyperef/subvif.fasta
argchoice:subvpr.fasta:/database/DNA/subtyperef/subvpr.fasta
argchoice:subvpu.fasta:/database/DNA/subtyperef/subvpu.fasta
argchoice:subnef.fasta:/database/DNA/subtyperef/subnef.fasta

out:OUTPUTFILE
outformat:genbank


item:HIV-1 Subtype reduz.
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:HIV Subtype C CG:/database/DNA/sub-reference/subC.CG.fasta
argchoice:HIV-1 GAG sub:/database/DNA/sub-reference/gagsub-reference.fasta
argchoice:HIV-1 POL sub:/database/DNA/sub-reference/polsub-reference.fasta
argchoice:HIV-1 VIF sub:/database/DNA/sub-reference/vifsub-reference.fasta
argchoice:HIV-1 VPR sub:/database/DNA/sub-reference/vprsub-reference.fasta
argchoice:HIV-1 TAT sub:/database/DNA/sub-reference/tatsub-reference.fasta
argchoice:HIV-1 REV sub:/database/DNA/sub-reference/revsub-reference.fasta
argchoice:HIV-1 VPU sub:/database/DNA/sub-reference/vpusub-reference.fasta
argchoice:HIV-1 ENV sub:/database/DNA/sub-reference/envsub-reference.fasta
argchoice:HIV-1 NEF sub:/database/DNA/sub-reference/nefsub-reference.fasta

out:OUTPUTFILE
outformat:genbank

item:HIV-1 Subtype B & C Gen. regions
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:HIV Subtype C CG:/database/DNA/subB/$format.fasta
argchoice:HIV-1 GAG sub:/database/DNA/subB/$format.gag$type.fasta
argchoice:HIV-1 POL sub:/database/DNA/subB/$format.pol$type.fasta
argchoice:HIV-1 PROTEASE sub:/database/DNA/subB/$format.pol-prot$type.fasta
argchoice:HIV-1 RT sub:/database/DNA/subB/$format.pol-RT$type.fasta
argchoice:HIV-1 INTEGRASE sub:/database/DNA/subB/$format.pol-INT$type.fasta
argchoice:HIV-1 VIF sub:/database/DNA/subB/$format.vif$type.fasta
argchoice:HIV-1 VPR sub:/database/DNA/subB/$format.vpr$type.fasta
argchoice:HIV-1 TAT sub:/database/DNA/subB/$format.tat$type.fasta
argchoice:HIV-1 REV sub:/database/DNA/subB/$format.rev$type.fasta
argchoice:HIV-1 VPU sub:/database/DNA/subB/$format.vpu$type.fasta
argchoice:HIV-1 ENV sub:/database/DNA/subB/$format.env$type.fasta
argchoice:HIV-1 NEF sub:/database/DNA/subB/$format.nef$type.fasta

arg:format
argtype:chooser
arglabel:Format
argchoice:Subtype B:subB
argchoice:Subtype C:subC

arg:type
argtype:chooser
arglabel:type
argchoice:DNA:
argchoice:AA:AA

out:OUTPUTFILE
outformat:genbank


item:Find Beggining of Genome regions
itemmethod:findall $SEARCH $PRCNT $CASE $UT -match $MAT -mismatch $MIS < in1 > out1;
itemhelp:findall.help 
itemmeta:f
 
arg:SEARCH
argtype:choice_list
argchoice:Protease:ATCACTCTTTGG
argchoice:Protease:ATC
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:hivHXB2 genome regions aln
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:/database/DNA/hivHXB2regions.fasta

out:OUTPUTFILE
outformat:genbank

menu:Protein


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


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 /var/www/cgi-bin/db/PAM30; /usr/local/biotools/blast/blastall -p blastp -d $BLASTDB -i in1.f -W $WORDLEN -M $Matrix > in1.tmp; /usr/openwin/bin/textedit in1.tmp; rm in1* PAM30)&


in:in1
informat:flat
insave:

arg:BLASTDB
argtype:choice_list
arglabel:Which Database
argchoice:HIV Proteins Tulio:/var/www/cgi-bin/db/HIV-PROTEINS-tulio.fasta
argchoice:HIV Proteins:/var/www/cgi-bin/db/hiv17-08-01.PROT.fasta
argchoice:HIV-1 Structures at PDB:/var/www/cgi-bin/db/Prot.3d.fasta
argchoice:local:$GDE_HELP_DIR/BLAST/local_db

arg:Matrix
barglabel:Substitution Matrix:
argtype:choice_list
argchoice:PAM30:PAM30
argchoice:PAM70:PAM70

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

item:tblastn
itemmethod:(sed "s/[#%]/>/" <in1 > in1.f; cp /var/www/cgi-bin/db/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:PAM30:PAM30
argchoice:PAM70:PAM70

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:VESPA PROTEASE
itemmethod:cat in1 > infile ;/usr/local/biotools/GDE/bin/fasta2VESPA.pl > outfile; sed "s/[%]/ /" <outfile > outfile.f ;/home/tulio/biotools/VESPA/VESPA -b $SUBTYPE -q outfile.f > outVESPA; textedit outVESPA;

arg:SUBTYPE
argtype:chooser
arglabel:Subtype
argchoice:B:/database/AA/subB.prot.aa.vespa
argchoice:C:/database/AA/subC.prot.aa.vespa
argchoice:D:/database/AA/subD.prot.aa.vespa
in:in1
informat:flat
out:out1
outformat:text

item:VESPA Reverse Transcriptase
itemmethod: cat in1 > infile ;/usr/local/biotools/GDE/bin/fasta2VESPA.pl > outfile; sed "s/[%]/ /" <outfile > outfile.f ;/home/tulio/biotools/VESPA/VESPA -b $SUBTYPE -q outfile.f > outVESPA; textedit outVESPA;

arg:SUBTYPE
argtype:chooser
arglabel:Subtype
argchoice:B:/database/AA/subB.rt.aa.vespa
argchoice:C:/database/AA/subC.rt.aa.vespa
argchoice:D:/database/AA/subD.rt.aa.vespa
in:in1
informat:flat
out:out1
outformat:text

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:Coalescence
itemmethod: (readseq -a -f11 in1 | sed "s/ YF//1" > infile2;cat tt infile2> infile; /usr/bin/X11/xterm -e  /usr/local/biotools/lamarc/coalesce/coalesce;)&
itemhelp:lsadt.help

in:in1
informat:genbank
insave:
inmask:

item:tree-puzzle
itemmethod: (readseq -a -f12 in1 > infile; /usr/bin/X11/xterm -e; (echo b; echo y) |  puzzle; textedit outfile; gv outlm.eps)&
itemhelp:lsadt.help

in:in1
informat:genbank
insave:
inmask:
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  /usr/bin/X11/xterm -e  $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:PAUP
itemmethod:(readseq -a -f17 in1 > work.nxs; /usr/bin/X11/xterm -e paup work.nxs;/bin/rm -f gde*)&

in:in1
informat:genbank
inmask:
insave:

item:MrBaynes
itemmethod:(readseq -a -f17 in1 | sed "s/interleave /interleave=yes /" > work.nxs;cat work.nxs /home/tulio/biotools/mbaynes/mbcommant.txt > workmb.nxs; /usr/bin/X11/xterm -e; (echo execute workmb.nxs) | mb workmb.nxs;treetool workmb.nxs.out.t; /bin/rm in1)&

in:in1
informat:genbank
inmask:
insave:

item:codeml
itemmethod:(readseq -a -f11 in1 | sed "s/ YF//1" > test.phy;  /usr/bin/X11/xterm -e  codeml $METHOD)&


arg:METHOD
arglabel:Which method ?
argtype:chooser
argchoice:0:/home/tulio/biotools/paml/method0.ctl
argchoice:1:/home/tulio/biotools/paml/method1.ctl
argchoice:2:/home/tulio/biotools/paml/method2.ctl
argchoice:3:/home/tulio/biotools/paml/method3.ctl
argchoice:4:/home/tulio/biotools/paml/method4.ctl
argchoice:5:/home/tulio/biotools/paml/method5.ctl
argchoice:6:/home/tulio/biotools/paml/method6.ctl


in:in1
informat:genbank
inmask:
insave:

  
item:Phylip Distance methods
itemmethod:(readseq -a -f12 in1 | sed "s/ YF//1" > infile ;$PROG mv -f outfile infile;  /usr/bin/X11/xterm -e dnadist;mv -f outfile infile;  /usr/bin/X11/xterm -e neighbor; cp outtree intree; $PROGRAM  textedit outfile;treetool outtree;/bin/rm -f in1 infile outfile)&
 
arg:PROGRAM
arglabel:Which method?
argtype:chooser
argchoice:DNADIST+NEIGHBOR:
argchoice:Fitch: /usr/bin/X11/xterm -e  fitch;
argchoice:Kitsch: /usr/bin/X11/xterm -e  kitsch;
argchoice:Neighbor: /usr/bin/X11/xterm -e  neighbor;
argchoice:Bootstrap+consense: /usr/bin/X11/xterm -e  consense;

arg:PROG
arglabel:Which method?
argtype:chooser
argchoice:Bootstrap: /usr/bin/X11/xterm -e  seqboot;
argchoice:No Bootstrap:

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

menu:On-Line Res.
item:Search Los Alamos DB Search
itemmethod:(netscape http://hiv-web.lanl.gov/cgi-bin/hivDB3/public/wdb/ssampublic)
arg:term
argtype:text 
arglabel:Search sequence accession 
argtext:
item:Search Entrez
itemmethod:(netscape http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=Entrez&term=$search)&

arg:search
argtype:text 
arglabel:Search Entrez
argtext:

item:Search PubMed
itemmethod:(netscape http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=PubMed&term=$term)&

arg:term
argtype:text 
arglabel:Search PubMed for Literature: 
argtext:

item:Online Resources at Retroviruses in NCBI
itemmethod:(netscape http://www.ncbi.nlm.nih.gov/retroviruses/)&

item:SNAP Analysis online (dn/ds)
itemmethod:(netscape http://hiv-web.lanl.gov/SNAP/WEBSNAP/SNAP.html)& 

item:RIP Analysis online (Recombination)
itemmethod:(netscape http://hiv-web.lanl.gov/RIP/RIP.html)& 

item:Search Stanford for Resistance mutations
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
inmask:
insave:

menu:Tree Viewer
item:TreeTool
itemmethod:(treetool &);
item:TreeView
itemmethod:(tv &);
item:Xsplit-tree
itemmethod:(/usr/local/biotools/splitstree3.1/xsplits &);













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


menu:Xylem
#------------ Open XYLEM Dataset (GenBank) ( 9/ 6/94) ---------------
item:Open_XYLEM (GenBank)
itemlabel:Open XYLEM Dataset (GenBank)
itemmethod:getloc $DBNAME.ind $DBNAME.ano $DBNAME.wrp $DBNAME.ind out1

arg:DBNAME
arglabel:XYLEM-format GenBank Dataset
argtype:text

out:out1
outformat:genbank

#-------------- Open XYLEM Database (PIR) ( 9/ 6/94) --------------
item:Open_XYLEM (PIR)
itemlabel:Open XYLEM Dataset (GenBank)
itemmethod:getloc -p $DBNAME.ind $DBNAME.ano $DBNAME.wrp $DBNAME.ind out1.pir; readseq -a -f2 out1.pir > out1

arg:DBNAME
arglabel:XYLEM-format PIR Dataset
argtype:text
#argtype:file_chooser

out:out1
outformat:genbank


#################################    PROTEIN   ################################
#--------------- PROT2NUC - Reverse Translation ( 8/10/94) -----------------
item:PROT2NUC - reverse translation
itemmethod: sed "s/[#%]/>/" <in1 | prot2nuc  -l$LINLEN -g$GROUP > in1.out; (textedit in1.out; rm in1*)&
itemhelp: xylem/prot2nuc.doc

arg:LINLEN
arglabel:CODONS PER LINE
argtype:slider
argmin:5
argmax:100
argvalue:25

arg:GROUP
arglabel:NUMBERING INTERVAL (amino acids/codons)
argtype:slider
argmin:5
argmax:100
argvalue:5

in:in1
informat:flat

########################### DATABASE MENU ###############################
#------------------- FINDKEY  (3/13/97)-----------------------
item:FINDKEY - Keyword Search
itemmethod: $KEYWORDS; (findkey $DATABASE in1.kw in1.nam in1.fnd; rm in1.kw; (textedit in1.fnd; rm in1.fnd)& (textedit in1.nam -Ws 150 628; rm in1.nam)&  )&
itemhelp:xylem/findkey.asc

arg:KEYWORDS
arglabel:KEYWORDS
argtype:chooser
argchoice:Single keyword:echo $KEY > in1.kw
argchoice:Create list of keywords:cat $GDE_HELP_DIR/xylem/GDE/keyfile.template > in1.tmp; textedit in1.tmp; egrep -v -e \; in1.tmp >in1.kw;rm in1.tmp*
argvalue:0

arg:KEY
arglabel:Single keyword
argtype:text

arg:DATABASE
arglabel:DATABASE
argtype:choice_menu
argchoice:HIV GB:-G /database/DNA/hiv1entries
argchoice:PIR:-p
argchoice:PIR Dataset:-P $DBFILE
argchoice:GB bacterial:-b
argchoice:GB mamalian:-m
argchoice:GB phage:-g
argchoice:GB primate:-r
argchoice:GB rodent:-d
argchoice:GB unannotated:-u
argchoice:GB vertebrate:-t
argchoice:GB invertebrate:-i
argchoice:GB plant:-l
argchoice:GB rna:-n
argchoice:GB synthetic:-s
argchoice:GB viral:-a
argchoice:GB patented:-x
argchoice:GB Seq. Tagged Sites:-z
argchoice:GB expressed seq. tag:-e
argchoice:GB Genome Survey Seq.:-S
argchoice:GB High Throughput Genomic:-h
argchoice:GenBank Dataset:-G $DBFILE
argchoice:VecBase:-v
argvalue:0

arg:DBFILE
arglabel:Dataset name
argtype:text

in:in1
informat:flat

#------------------- FETCH ( 2/ 7/94) --------------------------
# Note: This menu requires that the shell script 'GBfilter' be
# in your bin directory.
item:FETCH
itemmethod: $NAMES; (fetch $WHATTOGET $DATABASE in1.nam in1.tmp; rm in1.nam; $WHERE) &
itemhelp:xylem/fetch.doc

arg:NAMES
arglabel:NAMES/ACCESSION #'S
argtype:chooser
argchoice:Single name/acc:echo $NAMEFILE > in1.nam
argchoice:Create list of names/acc#'s:cat $GDE_HELP_DIR/xylem/GDE/namefile.template > in1.tmpname; textedit in1.tmpname; egrep -v -e \; in1.tmpname >in1.nam;rm in1.tmpname* 
argchoice:File of Names/Acc.#'s:cat $NAMEFILE >in1.nam
argvalue:0

arg:NAMEFILE
arglabel:Single name, accession # or file of names/acc. #'s
argtype:text

arg:WHATTOGET
arglabel:WHAT TO GET
argtype:chooser
argchoice:annotation:-a
argchoice:sequence:-s
argchoice:both:-b
argvalue:2

arg:DATABASE
arglabel:DATABASE
argtype:chooser
argchoice:GenBank:-g
argchoice:GenBank Dataset:-G $DBFILE
argchoice:HIV Dataset:-G /database/DNA/hiventries
argchoice:PIR:-p
argchoice:PIR Dataset:-P $DBFILE
argchoice:VecBase:-v
argvalue:0

arg:DBFILE
arglabel:Dataset
argtype:text

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
# If GenBank file, read directly, otherwise, convert to GenBank.
argchoice:GDE:(GBfilter in1.tmp in1.gen; gde in1.gen; rm in1.*)&
argchoice:Textedit window:(textedit in1.tmp;rm in1.tmp) &
argchoice:Output file:mv in1.tmp $OUTFILE; echo ' Fetch completed'
argchoice:GenBank Dataset:splitdb -g in1.tmp $OUTFILE.ano $OUTFILE.wrp $OUTFILE.ind; rm in1.*; echo ' Fetch completed'
argchoice:PIR Dataset:splitdb -p in1.tmp $OUTFILE.ano $OUTFILE.wrp $OUTFILE.ind; rm in1.*; echo ' Fetch completed'
argvalue:0

arg:OUTFILE
arglabel:Output file or Dataset name
argtype:text

in:in1
informat:genbank

out:OUTPUT
outformat:genbank

#----------------  FEATURES - by feature key ( 3/14/94)  -------------------
item:FEATURES - Extract by feature keys
# sed corrects errors in GDE-generated genbank output
itemmethod: sed -e "s/^LOCUS */LOCUS       /" -e "s/^ ACCESSION/ACCESSION /" -e "/^$/d"  in1 > in1.gen; $FEALIST; ($FCOMMAND -F in1.feafile $DATABASE; rm in1.feafile in1.efile in1.gen; $WHERE) & 
itemhelp:xylem/features.doc

arg:FEALIST
arglabel:FEATURES TO EXTRACT
argtype:chooser
argchoice:Single feature:echo $FEAKEY > in1.feafile
argchoice:Create list of features:cat $GDE_HELP_DIR/xylem/GDE/feafile.template > in1.tmpfeafile; textedit in1.tmpfeafile; egrep -v -e \; in1.tmpfeafile >in1.feafile; rm in1.tmpfeafile 
argvalue:0

arg:FEAKEY
arglabel:Single feature key
argtype:choice_list
argchoice:allele:allele
argchoice:attenuator:attenuator
argchoice:binding:binding
argchoice:CAAT_signal:CAAT_signal
argchoice:CDS:CDS
argchoice:chromosome:chromosome
argchoice:conflict:conflict
argchoice:contig:contig
argchoice:C_region:C_region
argchoice:D_loop:D_loop
argchoice:D_region:D_region
argchoice:D_segment:D_segment
argchoice:enhancer:enhancer
argchoice:exon:exon
argchoice:GC_signal:GC_signal
argchoice:iDNA:iDNA
argchoice:intron:intron
argchoice:J_region:J_region
argchoice:J_segment:J_segment
argchoice:LTR:LTR
argchoice:mat_peptide:mat_peptide
argchoice:misc_binding:misc_binding
argchoice:misc_difference:misc_difference
argchoice:misc_feature:misc_feature
argchoice:misc_recomb:misc_recomb
argchoice:misc_RNA:misc_RNA
argchoice:misc_signal:misc_signal
argchoice:misc_structure:misc_structure
argchoice:modified_base:modified_base
argchoice:mRNA:mRNA
argchoice:mutation:mutation
argchoice:N_region:N_region
argchoice:old_sequence:old_sequence
argchoice:polyA_signal:polyA_signal
argchoice:polyA_site:polyA_site
argchoice:precursor_RNA:precursor_RNA
argchoice:primer_bind:primer_bind
argchoice:prim_transcript:prim_transcript
argchoice:promoter:promoter
argchoice:protein_bind:protein_bind
argchoice:RBS:RBS
argchoice:repeat_region:repeat_region
argchoice:repeat_unit:repeat_unit
argchoice:rep_origin:rep_origin
argchoice:rRNA:rRNA
argchoice:satellite:satellite
argchoice:scRNA:scRNA
argchoice:sig_peptide:sig_peptide
argchoice:snRNA:snRNA
argchoice:source:source
argchoice:S_region:S_region
argchoice:stem_loop:stem_loop
argchoice:STS:STS
argchoice:TATA_signal:TATA_signal
argchoice:terminator:terminator
argchoice:transit_peptide:transit_peptide
argchoice:tRNA:tRNA
argchoice:unsure:unsure
argchoice:variation:variation
argchoice:virion:virion
argchoice:V_region:V_region
argchoice:V_segment:V_segment
argchoice:3'clip:3\'clip
argchoice:3'UTR:3\'UTR
argchoice:5'UTR:5\'UTR
argchoice:5'clip:5\'clip
argchoice:-10_signal:-10_signal
argchoice:-35 signal:-35 signal
argvalue:5

arg:FCOMMAND
arglabel:NAMES/ACCESSION #'S OF ENTRIES
argtype:choice_menu
argchoice:Single name:echo $EFILE > in1.efile; features -N in1.efile
argchoice:Create list of names:cat $GDE_HELP_DIR/xylem/GDE/names.template > in1.tmpefile; textedit in1.tmpefile; egrep -v -e \; in1.tmpefile >in1.efile; rm in1.tmpefile; features -N in1.efile
argchoice:File of names:cat $EFILE >in1.efile; features -N in1.efile
argchoice:Single Acc#:echo $EFILE > in1.efile; features -A in1.efile
argchoice:Create list of Acc#s:cat $GDE_HELP_DIR/xylem/GDE/acc.template > in1.tmpefile; textedit in1.tmpefile; egrep -v -e \; in1.tmpefile >in1.efile; rm in1.tmpefile; features -A in1.efile
argchoice:File of Acc#s:cat $EFILE >in1.efile; features -A in1.efile
argvalue:0

arg:EFILE
arglabel:Name, Accession # or filename
argtype:text

arg:DATABASE
arglabel:DATABASE
argtype:chooser
argchoice:GenBank:-g
argchoice:GenBank Dataset:-u $DBFILE
argchoice:Selected sequences:-U in1.gen
argvalue:0

arg:DBFILE
arglabel:Dataset name
argtype:text

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:GDE:readseq -a -f2 in1.out >in1.result; (gde in1.result;rm in1.*)&
argchoice:Textedit windows:(textedit in1.msg -Ws 450 350;rm in1.msg)& (textedit in1.exp -Ws 350 350; rm in1.exp) & (textedit in1.out -Ws 400 350;rm in1.out)&  
argchoice:Output file:mv in1.msg $OUTNAME.msg; mv in1.out $OUTNAME.out; mv in1.exp $OUTNAME.exp; echo 'Features completed'
argvalue:0

arg:OUTNAME
arglabel:Output file name
argtype:text

in:in1
informat:genbank

out:RESULT
outformat:genbank

#--------------------  FEATURES - by expression ( 3/14/94)---------------------
item:FEATURES - Extract using expressions
itemmethod: $CHOOSEEXP; sed -e "s/^LOCUS */LOCUS       /" -e "s/^ ACCESSION/ACCESSION /" -e "/^$/d"  in1 > in1.gen; (features -E in1.efile $DATABASE; rm in1.gen in1.efile; $WHERE)& 
itemhelp:xylem/features.doc

arg:CHOOSEEXP
arglabel:EXPRESSION(S)
argtype:chooser
argchoice:Single expression:echo '$EXPRESSION'|cut -f1 -d":" > in1.accfile; echo \>`cat in1.accfile` >in1.efile; echo '@$EXPRESSION' >> in1.efile; rm in1.accfile
argchoice:Expression file:cat $EFILE >in1.efile
argchoice:Create list of expressions:cat $GDE_HELP_DIR/xylem/GDE/expfile.template > in1.tmpexpfile; textedit in1.tmpexpfile; egrep -v -e \; in1.tmpexpfile >in1.efile; rm in1.tmpexpfile 
argvalue:0

arg:EXPRESSION
arglabel:Feature expression
argtype:text

arg:EFILE
arglabel:Expression file
argtype:text

arg:DATABASE
arglabel:DATABASE
argtype:chooser
argchoice:GenBank:-g
argchoice:GenBank Dataset:-u $DBFILE
argchoice:Selected sequences:-u in1.gen
argvalue:0

arg:DBFILE
arglabel:Dataset name
argtype:text

arg:WHERE
arglabel:WHERE TO SENT OUTPUT
argtype:chooser
argchoice:GDE:readseq -a -f2 in1.out >in1.result; (gde in1.result;rm in1.*)&
argchoice:Textedit windows:(textedit in1.msg -Ws 450 350;rm in1.msg)& (textedit in1.out -Ws 400 350;rm in1.out)&
argchoice:Output file:mv in1.msg $OUTNAME.msg; mv in1.out $OUTNAME.out;echo 'Features completed'
argvalue:0

arg:OUTNAME
arglabel:Output file name
argtype:text

in:in1
informat:genbank

out:RESULT
outformat:genbank

######################## ALIGNMENT MENU ###############################
#--------------- REFORM - print multiple alignment (2/ 2/95) -----------------
item:REFORM - print mult. align.
#Note: do not use flat or gde .
itemmethod:(cat in1 |readseq -pipe -a -f8 | reform $TYPE -fp $GAPS $CAPS $DOTS -l$LINESIZE -s$START > in1.out; textedit in1.out;rm in1*) &
itemhelp: xylem/reform.doc

arg:TYPE
argtype:chooser
arglabel:Type:
argchoice:Protein:
argchoice:Nucleic acid:-n
argvalue:0

arg:GAPS
argtype:chooser
arglabel:Print gaps as
argchoice:Dashes:-g
argchoice:Spaces:
argvalue:0

arg:CAPS
argtype:chooser
arglabel:Capitalize conserved sites in consensus seq.
argchoice:Yes:-c
argchoice:No:
argvalue:0

arg:DOTS
argtype:chooser
arglabel:Print conserved sites in alignment as dots
argchoice:Yes:-p
argchoice:No:
argvalue:0
 
arg:LINESIZE
arglabel:# residues per line
argtype:slider
argmin:40
argmax:150
argvalue:70

arg:START
arglabel:Begin numbering at
argtype:slider
argmin:-500000
argmax:500000
argvalue:1

in:in1
#informat:flat
informat:genbank
insave:


############################## SIMILARITY MENU ############################
#--------------- SHUFFLE - randomize sequences (11/10/93) -----------------
item:SHUFFLE - randomize sequences
itemmethod: sed "s/[#%]/>/" <in1 >in1.tmp; shuffle -s$SEED -w$WINDOW -o$OVERLAP <in1.tmp |tail +3> in1.shuf; readseq -a -f2 in1.shuf >out1; rm in1*
itemhelp: xylem/shuffle.doc

arg:SEED
arglabel:RANDOM SEED
argtype:slider
argmin:1
argmax:32767
argvalue:7777

arg:WINDOW
arglabel:WINDOW
argtype:slider
argmin:5
argmax:500000
argvalue:10

arg:OVERLAP
arglabel:OVERLAP BETWEEN ADJACENT WINDOWS
argtype:slider
argmin:0
argmax:100
argvalue:0

in:in1
informat:flat

out:out1
outformat:genbank