# .GDEmenus for Linux-Intel 
# This file was automatically generated by makemenus.py.
# Changes should be made to individual .item files,
# and the .GDEmenus file re-created using makemenus.py.
############################################################################
#                                                                          #
#                                                                          #
#         ####   #####   ######  #    #  ######  #    #  #    #   ####     #
#        #    #  #    #  #       ##  ##  #       ##   #  #    #  #         #
#        #       #    #  #####   # ## #  #####   # #  #  #    #   ####     #
#        #  ###  #    #  #       #    #  #       #  # #  #    #       #    #
#    ### #    #  #    #  #       #    #  #       #   ##  #    #  #    #    #
#    ###  ####   #####   ######  #    #  ######  #    #   ####    ####     #
#                                                                          #
#       .GDEmenus 1993 by Steven Smith                                     #
#       .GDEmenus Version   3/27/2003  by Brian Fristensky                 #
#                                                                          #
############################################################################

# 3/27/03 - To simplify GDE_HELP_DIR, all help files are now reached
#   through $GDE_HELP_DIR/doc, which is a symbolic link to $DOC.
#   Thus, the only files remaining in GDE_HELP_DIR are .GDEmenus
#   and some symbolic links.

# 7/24/02 Standardized use of environment variables required by .GDEmenus.
# eg. calls to the $GDE_TEXTEDIT editor are replaced by the environment variable $GDE_TEXTEDIT
# $doc changed to $DOC, $dat changed to $DAT. It's a good idea to set $GDE_TEXTEDIT
# to an editor that supports the X11 '-geometry' option controlling window size
# see ('man X'). Such editors include the CDE dtpad editor, nedit, and xemacs.
# gedit and fox don't support this option.
#
# $GDE_TERM lists the terminal to use when running a command line program
# It should include the appropriate command-line option for sending a
# command to the terminal program.
# eg. in CDE, $GDE_TERM = 'dtterm -e ' or 'xterm -e '

# 6/25/2001 - Extensively modified a large number of menuitems to
# conform to the Java re-write of readseq (2.1.3). The most important
# difference is that the original C version allowed commands of the
# form 'readseq infile > outfile. The Java version does not send
# output to the standard output. Therefore, commands have changed to
# use the output option 'readseq infile -o=outfile'.
# Note: the "=" sign is needed in "-o=file" expressions for 
# backward compatibility with the original readseq.

#
####################################################################
# This version of .GDEmenus drastically expands the capabilities of 
# GDE. The best way to find out what it can do is to install GDE,
# and then install this file as your .GDEmenus file. None of the programs
# this file calls will work until installed and configured,
# but you can get a quick idea of the look and feel of the menus 
# before you do an installation. Each menu item is stand alone, so
# you can pick and choose which ones you want, to customize GDE for
# your local setup.

# Note: Previous versions of this file called the OpenWindows 'textedit'
# program as its text editor. Since CDE is now the default window
# system on Suns, the CDE $GDE_TEXTEDIT editor is now called. If your
# system does not yet have CDE, change '$GDE_TEXTEDIT' to 'textedit' throughout
# this file. Also, calls to shelltool have been changed to call dtterm.


############################## File ##############################
menu:File

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

out:out1
outformat:flat

#------------ SPLITDB ( 2/11/05) ---------------
item:SPLITDB - GenBank/PIR to XYLEM dataset
itemlabel:SPLITDB - GenBank/PIR to XYLEM dataset
itemmethod:splitdb $DBTYPE $SPECIESINFO $COMPRESSION $FILENAME $DBNAME.ano $DBNAME.wrp $DBNAME.ind
itemhelp:doc/xylem/splitdb.txt
itemopen:gde_help_viewer.csh

arg:FILENAME
arglabel:GenBank/PIR file
argtype:text
#argtype:file_chooser

arg:DBTYPE
argtype:chooser
arglabel:Input file type
argchoice:GenBank (.gen):
argchoice:PIR (.pir):-p
argvalue:0

arg:DBNAME
arglabel:Name for XYLEM-format GenBank Dataset
argtype:text
argtext:dataset

arg:SPECIESINFO
argtype:chooser
arglabel:Include species name in index (.ind)? (GenBank only)
argchoice:Yes:-t
argchoice:No:
argvalue:0

arg:COMPRESSION
argtype:chooser
arglabel:Compress leading blanks in annotation (.ano)?
argchoice:Yes:-c
argchoice:No:
argvalue:1


#------------ 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) (11/05/00) --------------
item:Open_XYLEM (PIR)
itemlabel:Open XYLEM Dataset (GenBank)
itemmethod:getloc -p $DBNAME.ind $DBNAME.ano $DBNAME.wrp $DBNAME.ind out1.pir; readseq -a -fGenBank -o=out1 out1.pir

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

out:out1
outformat:genbank

#--------------------- Import Foreign Format  (11/ 5/00) -------------------
item:Import Foreign Format
itemmethod:cp $INPUTFILE OUTFILE.tmp; readseq -a -fGenBank -o=OUTPUTFILE OUTFILE.tmp; $RM_CMD -f OUTFILE.tmp
itemhelp:readseq.help
itemopen:gde_help_viewer.csh

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

out:OUTPUTFILE
outformat:genbank

#------------------ Import Free Format (FSAP)  ( 2/ 8/05) -------------------

item:Import Free Format (FSAP)
itemmethod: free2gb.csh $INPUTFILE out1;
itemhelp:doc/fsap/funnel.txt
itemopen:gde_help_viewer.csh

arg:INPUTFILE
argtype:text
arglabel:Name of Free Format (FSAP) file?

out:out1
outformat:genbank


#-------------  Export Foreign Format  (11/05/00)   ---------------------
#
# Formats now compatible with readseq2 (Java)
#
# BF - changes all leading ~'s in alignment to -'s, which is more
# useful when working with multiple alignments.
item:Export Foreign Format
itemmethod:(tr "~" "-" <in1 > in1.out; readseq -all -form=$FORMAT -o=$OUTPUTFILE in1.out; $RM_CMD in1*)
itemhelp:readseq.help
itemopen:gde_help_viewer.csh

arg:FORMAT
argtype:choice_menu
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:phylip2
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
argchoice:XML:xml
#argchoice:BLAST:blast
#argchoice:SCF:scf
#argchoice:ASN.1:asn.1

arg:OUTPUTFILE
argtype:text
arglabel:Save as?

in:in1
informat:genbank
insave:

#--------------------------- Pretty PrinT -------------------------------------
#dgg addition for new readseq, 05 Nov 00
#

item:Pretty Print
itemmethod:readseq in1 -p -a -f=pretty $NAMELEFT $NAMERIGHT $NUMTOP $NUMBOT $NUMLEFT $NUMRIGHT -col=$COLS -width=$WIDTH $MATCH $GAPC -o=in1.pretty; ($GDE_TEXTEDIT in1.pretty; $RM_CMD -f in1 in1.pretty)&
itemhelp:readseq.help
itemopen:gde_help_viewer.csh

#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


#-------------------------------- Save selection --------------------------
item:Save Selection
itemmethod: cat $SAVE_FUNC > $Name
itemhelp:doc/GDE/save_selection.help
itemopen:gde_help_viewer.csh

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

#------------------------------ Print selection ----------------------------
item:Print Selection
itemmethod:(PrintStrat -in in1 -scale $SCALE > in1.tmp; $CMD -P$PRINTER in1.tmp; $RM_CMD -f in1 in1.tmp)&
itemhelp:doc/GDE/print_alignment.help
itemopen:gde_help_viewer.csh
 
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
argvalue:0 

arg:PRINTER
argtype:chooser
arglabel:Which printer?
argchoice:EPSON:$PRINTER
#argchoice:MACHRAY:machray
argchoice:copyctr:copyctr
argchoice:BLDGAGRIC.PLANT_HP3SI:bldgagric.plant_hp3si
 
in:in1
informat:gde
insave:


############################## Documentation ##############################
menu:Documentation

# ----------------------   DOCUMENTATION    ----------------------------


item:ViewDocumentation
itemmethod:($DOCUMENT)&

arg:DOCUMENT
arglabel:Documentation file
argtype:choice_menu
argchoice:GDE Documentation:$birch/script/browser.csh $tutorials/GDE/gde.html
argchoice:GDE Interface Documentation:$birch/script/browser.csh $tutorials/GDE/overview/GDE.interfaces.html#GDE
argchoice:GDE Manual:$GDE_PDFVIEW $DOC/GDE/GDE2.2_manual.pdf
argchoice:Ambiguity codes:$GDE_TEXTEDIT $DOC/Ambiguity_Codes.asc
argchoice:Amino acid codes:$GDE_TEXTEDIT $DOC/Amino_Acid_Codes.asc
argchoice:Genetic code:$GDE_TEXTEDIT $DAT/fsap/ugc.dat
argchoice:Restriction enzymes:$GDE_TEXTEDIT $DAT/REBASE/type2.lst
argchoice:GenBank:$GDE_TEXTEDIT $DOC/GenBank/gbrel.txt
argchoice:PIR:$GDE_TEXTEDIT $DOC/PIR/0protein_doc.codata
argvalue:0


############################## Edit ##############################
menu:Edit

# -------------------------------   sort    --------------------------------
item:Sort
itemmethod:(heapsortHGL in1 $PRIM_KEY $SEC_KEY > in1.tmp ; gde in1.tmp;$RM_CMD -f in1*)&
itemhelp:heapsortHGL.help
itemopen:gde_help_viewer.csh

arg:PRIM_KEY
argtype:choice_menu
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_menu
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:

# ----------------------- Copy out ( 1/17/94)  ----------------------------
item:Copy out
itemmethod:sed -e "s/^LOCUS   /LOCUS/" -e "s/^ ACCESSION/ACCESSION /" -e "/^$/d"  in1 > $HOME/.GDEclipboard

in:in1
informat:genbank

# ----------------------- Paste in  1/17/94) ----------------------------
item:Paste in
itemmethod:cp $HOME/.GDEclipboard out1

out:out1
outformat:genbank

# -------------------------------- Extract --------------------------------
item:extract
itemmethod:(gde in1;$RM_CMD -f in1)&

in:in1
informat:gde
insave:



############################## DNA/RNA ##############################
menu:DNA/RNA

#---------------------------- Assemble contigs  -------------------------------
item:Assemble Contigs
itemmethod:(sed "s/#/>/"<in1 >in1.tmp; CAP2 in1.tmp $OVERLAP $PMATCH > out1;$RM_CMD -f in1.tmp)
itemhelp:doc/GDE/CAP2.help
itemopen:gde_help_viewer.csh

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:

#------------------------- NUMSEQ ( 2/ 8/05) --------------------------
item:NUMSEQ - number a sequence

# INSTALLATION NOTE: The $GDE_HELP_DIR must contain a directory called 
# fsapdat that contains the genetic code files eg. ugc.dat These files contain
# the genetic codes as described in the FSAP documentation. 
# If you already have FSAP installed elsewhere, simply create a 
# symbolic link in the $GDE_HELP_DIR. For example:
# ln -s $DAT/fsap fsapdat
# will create a symbolic link to $DAT/fsap using the name fsapdat

# The directory fsapdoc must also be available in the $GDE_HELP_DIR,
# containing the file numseq.asc from the FSAP package. Again, this
# directory can be implemented as a symbolic link.
itemmethod: (numseq.csh in1 in1.out $GCFILE $START $FINISH $NUCCASE $SNUM $GROUP $GPL $WHICH $STRANDS $KIND $NUMBERS $NUCS $PEPTIDES $FRAMES $FORM; $RM_CMD in1; ($GDE_TEXTEDIT in1.out; $RM_CMD in1*) & )&
itemhelp:doc/fsap/numseq.txt
itemopen:gde_help_viewer.csh


arg:START
argtype:slider
arglabel:START
argmin:1
argmax:500000
argvalue:1

arg:FINISH
argtype:slider
arglabel:FINISH
argmin:1
argmax:500000
argvalue:500000

arg:NUCCASE
argtype:chooser
argchoice:UPPERCASE:U
argchoice:lowercase:l
argvalue:0

arg:SNUM
argtype:slider
arglabel:Number of starting nucleotide
argmin:-500000
argmax:500000
argvalue:0

arg:GROUP
argtype:slider
arglabel:write in GROUPs of
argmin:1
argmax:100
argvalue:10

arg:GPL
argtype:slider
arglabel:number of GROUPs printed per line
argmin:1
argmax:20
argvalue:7

arg:WHICH
arglabel:Which strand?
argtype:chooser
argchoice:original:i
argchoice:opposite:o
argvalue:0

arg:STRANDS
argtype:chooser
argchoice:One strand:1
argchoice:Both strands:2
argvalue:0

arg:KIND
argtype:chooser
arglabel:Print as
argchoice:DNA:D
argchoice:RNA:R
argvalue:0

arg:NUMBERS
arglabel:Numbering
argtype:chooser
argchoice:YES:Y
argchoice:NO:N
argvalue:0

arg:NUCS
arglabel:Print nucleotides
argtype:chooser
argchoice:YES:Y
argchoice:NO:N
argvalue:0

arg:PEPTIDES
argtype:chooser
arglabel:TRANSLATION
argchoice:YES:Y
argchoice:NO:N
argvalue:1

arg:FRAMES
argtype:chooser
arglabel:Reading frames
argchoice:One:1
argchoice:Three:3
argvalue:0

arg:FORM
argtype:chooser
arglabel:aa code
argchoice:Three letter:L
argchoice:One letter:S
argvalue:1

arg:GCFILE
argtype:choice_menu
arglabel:Genetic Code
argchoice:Standard:$DAT/fsap/gc/1.standard.gc
argchoice:Vertebrate Mitochondrial:$DAT/fsap/gc/2.vert_mito.gc
argchoice:Yeast Mitochondrial:$DAT/fsap/gc/3.yeast_mito.gc
argchoice:Mold, Protozoan, and Coelenterate Mitochondrial:$DAT/fsap/gc/4.MPC.mito.gc
argchoice:Invertebrate Mitochondrial:$DAT/fsap/gc/5.inv_mito.gc
argchoice:Ciliate, Dasycladacean and Hexamita:$DAT/fsap/gc/6.CDH.gc
argchoice:Echinoderm and Flatworm:$DAT/fsap/gc/9.EF_mito.gc
argchoice:Euplotid:$DAT/fsap/gc/10.Euplotid.gc
argchoice:Bacterial and Plant Plastid:$DAT/fsap/gc/11.Bact_Plastid.gc
argchoice:Alternative Yeast Nuclear:$DAT/fsap/gc/12.alt_yeast.gc
argchoice:Ascidian Mitochondrial:$DAT/fsap/gc/13.Ascidian_mito.gc
argchoice:Alternative Flatworm Mitochondrial:$DAT/fsap/gc/14.alt_flatworm_mito.gc
argchoice:Blepharisma:$DAT/fsap/gc/15.Blepharisma.gc
argchoice:Chlorophycean Mitochondrial:$DAT/fsap/gc/16.Chlorophycean_mito.gc
argchoice:Trematode Mitochondrial:$DAT/fsap/gc/21.Trematode_mito.gc
argchoice:Scenedesmus obliquus mitochondrial:$DAT/fsap/gc/22.Scenedesmus_mito.gc
argchoice:Thraustochytrium Mitochondrial:$DAT/fsap/gc/23.Thraustochytrium_mito.gc
argvalue:0

in:in1
informat:genbank
insave:

# ----------------  Translate --------------------------------
item:Translate...
itemmethod:Translate -tbl $TBL -frame $FRAME -min_frame $MNFRM $LTRCODE in1 $ALIGN > 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:ALIGN
argtype:chooser
arglabel:Align with DNA?
argchoice:Preserve codon spacing:
argchoice:No spaces between amino acids:|sed "s/--//g"
argvalue:1

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

# ----------------  Translate - Ribosome (2/11/05) ---------------------
item:Ribosome
itemmethod: readseq -a -ffasta -o=in1.out in1; cat in1.out | ribosome -g $GCFILE |egrep -v -e \; | tr '>' '%' > in1.ribosome; $RM_CMD -f in1.out; $GDEOUTPUT
itemhelp:doc/xylem/ribosome.txt
itemopen:gde_help_viewer.csh

in:in1
informat:genbank

arg:GCFILE
argtype:choice_menu
arglabel:Genetic Code
argchoice:Standard:$DAT/xylem/gc/1.standard.gc
argchoice:Vertebrate Mitochondrial:$DAT/xylem/gc/2.vert_mito.gc
argchoice:Yeast Mitochondrial:$DAT/xylem/gc/3.yeast_mito.gc
argchoice:Mold, Protozoan, and Coelenterate Mitochondrial:$DAT/xylem/gc/4.MPC.mito.gc
argchoice:Invertebrate Mitochondrial:$DAT/xylem/gc/5.inv_mito.gc
argchoice:Ciliate, Dasycladacean and Hexamita:$DAT/xylem/gc/6.CDH.gc
argchoice:Echinoderm and Flatworm:$DAT/xylem/gc/9.EF_mito.gc
argchoice:Euplotid:$DAT/xylem/gc/10.Euplotid.gc
argchoice:Bacterial and Plant Plastid:$DAT/xylem/gc/11.Bact_Plastid.gc
argchoice:Alternative Yeast Nuclear:$DAT/xylem/gc/12.alt_yeast.gc
argchoice:Ascidian Mitochondrial:$DAT/xylem/gc/13.Ascidian_mito.gc
argchoice:Alternative Flatworm Mitochondrial:$DAT/xylem/gc/14.alt_flatworm_mito.gc
argchoice:Blepharisma:$DAT/xylem/gc/15.Blepharisma.gc
argchoice:Chlorophycean Mitochondrial:$DAT/xylem/gc/16.Chlorophycean_mito.gc
argchoice:Trematode Mitochondrial:$DAT/xylem/gc/21.Trematode_mito.gc
argchoice:Scenedesmus obliquus mitochondrial:$DAT/xylem/gc/22.Scenedesmus_mito.gc
argchoice:Thraustochytrium Mitochondrial:$DAT/xylem/gc/23.Thraustochytrium_mito.gc
argvalue:0

arg:GDEOUTPUT
arglabel:Output to new GDE window?
argtype:chooser
# Problem with Linux-Intel version of GDE (doesn't affect Solaris):
# If we declare an 'out' file, then it must always exist,
# even if we don't use it. Otherwise, gde will look for the file
# after it is done, and crash.
argchoice:Yes:(echo '' > out1; gde in1.ribosome; $RM_CMD -f in1.ribosome)&
argchoice:No:mv in1.ribosome out1
argvalue:0

out:out1
outformat:flat

#----------------------------   Findall -----------------------------------
item:Find all <meta-f>
itemmethod:findall $SEARCH $PRCNT $CASE $UT -match $MAT -mismatch $MIS < in1 > out1;
itemhelp:doc/GDE/findall.help 
itemopen:gde_help_viewer.csh
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_menu
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:6
 
arg:MIS
argtype:choice_menu
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

#------------------------- BACHREST 4/09/06  --------------------------
item:BACHREST - Batch Rest. Site Search

# The directory fsapdoc must also be available in the $GDE_HELP_DIR,
# containing the file rest.asc from the FSAP package. Again, this
# directory can be implemented as a symbolic link.

itemmethod: (bachrest.csh in1 $DAT/REBASE/type2.lst in1.tmp $SOURCE $PROTO $PROT3 $BLUNT $PROT5 $SYMM $MINSITE $MAXSITE $FRAGLEAST $FRAGMOST $FRAGPRINT; ($GDE_TEXTEDIT in1.tmp; $RM_CMD in1*)& )&
itemhelp:doc/fsap/rest.txt
itemopen:gde_help_viewer.csh
itemopen:gde_help_viewer.csh

arg:SOURCE
argtype:chooser
arglabel:Source
argchoice:Commercial:C
argchoice:All:A
argvalue:1

arg:PROTO
argtype:chooser
arglabel:Prototypes only?
argchoice:Prototypes:P
argchoice:All:A
argvalue:0

arg:PROT3
argtype:chooser
arglabel:Include enzymes generating 3 prime protruding ends?
argchoice:Yes:Y
argchoice:No:N
argvalue:0

arg:BLUNT
argtype:chooser
arglabel:Include enzymes generating blunt ends?
argchoice:Yes:Y
argchoice:No:N
argvalue:0

arg:PROT5
argtype:chooser
arglabel:Include enzymes generating 5 prime protruding ends?
argchoice:Yes:Y
argchoice:No:N
argvalue:0

arg:SYMM
argtype:choice_menu
arglabel:Include
argchoice:Symmetric and Asymmetric sites:B
argchoice:Symmetric sites only:S
argchoice:Asymmetric sites only:A
argvalue:0

arg:MINSITE
argtype:slider
arglabel:Min. Recognition Seq. Length
argmin:4
argmax:21
argvalue:6

arg:MAXSITE
argtype:slider
arglabel:Max. Recognition Seq. Length
argmin:4
argmax:21
argvalue:21

arg:FRAGLEAST
argtype:slider
arglabel:Min. number of fragments generated
argmin:0
argmax:6000
argvalue:0

arg:FRAGMOST
argtype:slider
arglabel:Max. number of fragments generated
argmin:0
argmax:6000
argvalue:6000

arg:FRAGPRINT
argtype:slider
arglabel:Max. number of fragments printed
argmin:0
argmax:6000
argvalue:30

in:in1
informat:genbank
insave:

#------------------------- TACG (04/10/2006) --------------------------
item:TACG - restriction map (Version 3.6)

#itemmethod: (readseq -fgb -o=in1.tmp in1; python $BIRCH/script/tacg.py $TOPOLOGY $ORDER -n $MINSITE $OVERHANG -m $MINCUTS -M $MAXCUTS $REFILE -w $WIDTH $CUTS $FRAGS $LAMAP $LIMAP -g $MINFRAG,$MAXFRAG $TRANS $STRANDS --pdf $ADDITIONAL in1.tmp in1.out in1.pdf; $RM_CMD in1 in1.tmp; ($GDE_TEXTEDIT in1.out; $RM_CMD in1.out)& if [ -f in1.pdf ]; then ($GDE_PDFVIEW in1.pdf; $RM_CMD in1.pdf)& fi)&
itemmethod: (readseq -fgb -o=in1.tmp in1; python $BIRCH/script/tacg.py $TOPOLOGY $ORDER -n $MINSITE $OVERHANG -m $MINCUTS -M $MAXCUTS $REFILE -w $WIDTH $CUTS $FRAGS $LAMAP $LIMAP -g $MINFRAG,$MAXFRAG $TRANS $STRANDS -H --pdf $ADDITIONAL in1.tmp in1.html in1.pdf; $RM_CMD in1 in1.tmp; (browser.csh file://$PWD/in1.html)& if [ -f in1.pdf ]; then ($GDE_PDFVIEW in1.pdf; $RM_CMD in1.pdf in1.html)& fi)&
itemhelp:doc/tacg/tacg.main.html
itemopen:gde_help_viewer.csh

arg:TOPOLOGY
argtype:chooser
arglabel:Topology
argchoice:Linear:-f1
argchoice:Circular:-f0
argvalue:0

arg:ORDER
argtype:chooser
arglabel:Order by
argchoice:# of cuts:-c
argchoice:Alphabetical:
argvalue:1

arg:MINSITE
argtype:slider
arglabel:Min. Recognition Seq. Length
argmin:3
argmax:10
argvalue:6

arg:OVERHANG
argtype:chooser
arglabel:Overhang
argchoice:5 prime:-o5
argchoice:3 prime:-o3
argchoice:blunt:-o0
argchoice:all:-o1
argvalue:3

arg:MINCUTS
argtype:slider
arglabel:Min. cuts per sequence
argmin:0
argmax:100
argvalue:0

arg:MAXCUTS
argtype:slider
arglabel:Max. cuts per sequence
argmin:1
argmax:32000
argvalue:100

arg:REFILE
argtype:choice_menu
arglabel:Alt. Site file to search
argchoice:RE base (default):
argchoice:only REs that are Dam sensitive:-R $DAT/tacg/rebase.dam
argchoice:only REs that are Dcm sensitive:-R $DAT/tacg/rebase.dcm
argvalue:0

arg:CUTS
argtype:chooser
arglabel:print cut sites in tabular form
argchoice:Yes:-s
argchoice:No:
argvalue:0

arg:MINFRAG
argtype:slider
arglabel:PSEUDOGEL Min. frag. size (bp)
argmin:10
argmax:10000
argvalue:100

arg:MAXFRAG
argtype:slider
arglabel:PSEUDOGEL Max. frag. size (bp)
argmin:100
argmax:100000
argvalue:100000

arg:FRAGS
argtype:chooser
arglabel:PRINT FRAGMENTS?
argchoice:No:
argchoice:by position in map:-F1
argchoice:sorted by size:-F2
argchoice:both:-F3
argvalue:2

arg:LAMAP
argtype:chooser
arglabel:LADDER MAP?
argchoice:Yes:-l
argchoice:No:
argvalue:1

arg:LIMAP
argtype:chooser
arglabel:PRINT SEQUENCE AND SITES?
argchoice:Yes:-L
argchoice:No:
argvalue:1

arg:STRANDS
argtype:chooser
arglabel:strands
argchoice:one:--strands 1
argchoice:two:--strands 2
argvalue:0

arg:TRANS
argtype:choice_menu
arglabel:translation to accompany sequence
argchoice:none:
argchoice:1 frame, 1-letter code:-T1,1
argchoice:3 frames, 1-letter code:-T3,1
argchoice:6 frames, 1-letter code:-T6,1
argchoice:1 frame, 3-letter code:-T1,3
argchoice:3 frames, 3-letter code:-T3,3
argchoice:6 frames, 3-letter code:-T6,3
argvalue:0

arg:GC
argtype:choice_menu
arglabel:Genetic Code for translation
argchoice:Universal:-C0
argchoice:Vert. mitochondrial:-C1
argchoice:S. cerivisiae mitochondrial:-C2
argchoice:N. crassa mitochondrial:-C3
argchoice:Invertebrate mitochondrial:-C4
argchoice:Ciliate mitochondrial:-C5
argchoice:Euplotid mitochondrial:-C6
argchoice:Euplotid nuclear:-C7
argchoice:Bacterial:-C8
argchoice:Alt. Yeast:-C9
argchoice:Ascidian mitochondrial:-C10
argchoice:Flatworm:-C11
argchoice:Blepharisma:-C12
argvalue:0

arg:WIDTH
argtype:slider
arglabel:OUTPUT WIDTH (bp/line)
argmin:60
argmax:210
argvalue:60

arg:ADDITIONAL
argtype:text
arglabel:Additional options
argtext: 

in:in1
informat:genbank
insave:


############################## RNA_Struct ##############################
menu:RNA_Struct

#---------------------------- Draw Secondary Structure --------------------
item:Draw Secondary structure
itemmethod:(LoopTool $TEMPLATE in1 ; $RM_CMD -f in1) &
itemhelp:doc/GDE/LoopTool.help
itemopen:gde_help_viewer.csh

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

in:in1
informat:genbank
insave:loopout.ps


#----------------------- Highlight helix (5/27/00) -----------------------
item:Highlight helix
itemmethod:readseq -a -f8 -pipe in1 | sed "s/>HELIX/\"HELIX/" > in1.flat; sho_helix < in1.flat > out1;$RM_CMD in1.flat
itemhelp:doc/GDE/sho_helix.help
itemopen:gde_help_viewer.csh

in:in1
informat:genbank

out:out1
outformat:colormask




############################## Protein ##############################
menu:Protein

#----------------------------- GREASE (12/ 8/93)  ----------------------
item:GREASE - Kyte/Doolittle hydropathicity
itemmethod:(sed "s/[#%]/>/"<in1 >in1.seq;  grease in1.seq $WINDOW > in1.out; $GDE_TEXTEDIT in1.out; $RM_CMD in1*) &
itemhelp: doc/fasta/fasta20.asc
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

arg:WINDOW
arglabel:Window
argtype:slider
argmin:4
argmax:40
argvalue:7

#---------------------------- GARNIER (12/ 8/93)  ----------------------
item:GARNIER - secondary struct.
itemmethod:(sed "s/[#%]/>/"<in1 >in1.seq;  garnier in1.seq > in1.out; $GDE_TEXTEDIT in1.out; $RM_CMD in1*) &
itemhelp: doc/fasta/fasta20.asc
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

#--------------- PROT2NUC - Reverse Translation ( 2/11/05) -----------------
item:PROT2NUC - reverse translation
itemmethod: sed "s/[#%]/>/" <in1 | prot2nuc  -l$LINLEN -g$GROUP > in1.out; ($GDE_TEXTEDIT in1.out; rm in1*)&
itemhelp: doc/xylem/prot2nuc.txt
itemopen:gde_help_viewer.csh

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
insave:

#---------------------------------- PROSTAT ( 2/ 8/05)  ----------------------
item:Protein statistics
itemmethod:(sed "s/[#%]/>/"<in1 >in1.seq; dbstat < in1.seq > in1.out; $GDE_TEXTEDIT in1.out; rm in1*) &
itemhelp: doc/xylem/dbstat.txt
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:


############################## Similarity ##############################
menu:Similarity

#------------------------------ GGSEARCH  ( 5/14/08) ----------------------
item:GGSEARCH - Global/Global alignments
itemmethod:(sed "s/[#%]/>/"<in1 >in1.tmp; readseq -i1 -f8 in1.tmp -o=in1.seq1; readseq -i2 -f8 in1.tmp -o=in1.seq2; ggsearch3 -k $NUMSHUF $MATRIX $ZED $MARKX -E $EVALUE in1.seq1 in1.seq2  > in1.out; $GDE_TEXTEDIT in1.out; rm in1*) &
itemhelp: doc/fasta/fasta.txt
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

arg:MATRIX
arglabel:SCORING MATRIX
argtype:choice_menu
argchoice:Default:
argchoice:DNA matrix (DNA default):-s $DAT/fasta/dna.mat
argchoice:Blosum50 (Protein default):-s BL50
argchoice:Blosum62 (Protein):-s BL62
argchoice:Blosum80 (Protein):-s BL80
argchoice:PAM120 (Protein):-s P120
argchoice:PAM250 (Protein):-s P250
argchoice:MDM10 (Protein):-s M10
argchoice:MDM20 (Protein):-s M20
argchoice:MDM40 (Protein):-s M40
argvalue:0

arg:NUMSHUF
argtype:slider
arglabel:# OF RANDOMIZED TRIALS
argmin:1
argmax:10000
argvalue:500

arg:ZED
arglabel:Statistical model
argtype:choice_menu
argchoice:no statistics calculated:-z -1
argchoice:raw mean & SD; don't correct for lib. length:-z 0
argchoice:-z1 wt. regression; correct for lib. length (default):-z 1
argchoice:-z2 max. likelihood of Lambda and K:-z 2
argchoice:-z3 Altschul-Gish parameters:-z 3
argchoice:-z 4:-z 4
argchoice:-z 5:-z 5
argchoice:-z 6 composition-based maximumlikelihood:-z 6
argchoice:-z 11 (-z1 regession against randomly-suffled seqs):-z 11
argchoice:-z 12 (-z2 regession against randomly-suffled seqs):-z 12
argchoice:-z 14 (-z4 regession against randomly-suffled seqs):-z 14
argchoice:-z 15 (-z5 regession against randomly-suffled seqs):-z 15
argchoice:-z 16 (-z6 regession against randomly-suffled seqs):-z 16
argvalue:2

arg:MARKX
arglabel:DISPLAY
argtype:choice_menu
argchoice:Identity="colon" Cons. repl.="." Mismatch=" ":-m 0
argchoice:Identity=" " Cons. repl.="x" Mismatch="X":-m 1
argchoice:Print only 1st seq; Identity="." Mismatch="residue":-m 2
argchoice:graph of conserved positions:-m 4
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


#------------------------------ GLSEARCH  ( 5/14/08) ----------------------
item:GLSEARCH - Global/Local alignments
itemmethod:(sed "s/[#%]/>/"<in1 >in1.tmp; readseq -i1 -f8 in1.tmp -o=in1.seq1; readseq -i2 -f8 in1.tmp -o=in1.seq2; glsearch3 -k $NUMSHUF $MATRIX $ZED $MARKX -E $EVALUE in1.seq1 in1.seq2  > in1.out; $GDE_TEXTEDIT in1.out; rm in1*) &
itemhelp: doc/fasta/fasta.txt
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

arg:MATRIX
arglabel:SCORING MATRIX
argtype:choice_menu
argchoice:Default:
argchoice:DNA matrix (DNA default):-s $DAT/fasta/dna.mat
argchoice:Blosum50 (Protein default):-s BL50
argchoice:Blosum62 (Protein):-s BL62
argchoice:Blosum80 (Protein):-s BL80
argchoice:PAM120 (Protein):-s P120
argchoice:PAM250 (Protein):-s P250
argchoice:MDM10 (Protein):-s M10
argchoice:MDM20 (Protein):-s M20
argchoice:MDM40 (Protein):-s M40
argvalue:0

arg:NUMSHUF
argtype:slider
arglabel:# OF RANDOMIZED TRIALS
argmin:1
argmax:10000
argvalue:500

arg:ZED
arglabel:Statistical model
argtype:choice_menu
argchoice:no statistics calculated:-z -1
argchoice:raw mean & SD; don't correct for lib. length:-z 0
argchoice:-z1 wt. regression; correct for lib. length (default):-z 1
argchoice:-z2 max. likelihood of Lambda and K:-z 2
argchoice:-z3 Altschul-Gish parameters:-z 3
argchoice:-z 4:-z 4
argchoice:-z 5:-z 5
argchoice:-z 6 composition-based maximumlikelihood:-z 6
argchoice:-z 11 (-z1 regession against randomly-suffled seqs):-z 11
argchoice:-z 12 (-z2 regession against randomly-suffled seqs):-z 12
argchoice:-z 14 (-z4 regession against randomly-suffled seqs):-z 14
argchoice:-z 15 (-z5 regession against randomly-suffled seqs):-z 15
argchoice:-z 16 (-z6 regession against randomly-suffled seqs):-z 16
argvalue:2

arg:MARKX
arglabel:DISPLAY
argtype:choice_menu
argchoice:Identity="colon" Cons. repl.="." Mismatch=" ":-m 0
argchoice:Identity=" " Cons. repl.="x" Mismatch="X":-m 1
argchoice:Print only 1st seq; Identity="." Mismatch="residue":-m 2
argchoice:graph of conserved positions:-m 4
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


#------------------------------ LALIGN  ( 5/14/08) ----------------------
item:LALIGN - Best non-overlapping local alignments
itemmethod:(sed "s/[#%]/>/"<in1 >in1.tmp; readseq -i1 -f8 in1.tmp -o=in1.seq1; readseq -i2 -f8 in1.tmp -o=in1.seq2; lalign3 -k $NUMSHUF $MATRIX $ZED $MARKX -E $EVALUE in1.seq1 in1.seq2  > in1.out; $GDE_TEXTEDIT in1.out; rm in1*) &
itemhelp: doc/fasta/fasta.txt
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

arg:MATRIX
arglabel:SCORING MATRIX
argtype:choice_menu
argchoice:Default:
argchoice:DNA matrix (DNA default):-s $DAT/fasta/dna.mat
argchoice:Blosum50 (Protein default):-s BL50
argchoice:Blosum62 (Protein):-s BL62
argchoice:Blosum80 (Protein):-s BL80
argchoice:PAM120 (Protein):-s P120
argchoice:PAM250 (Protein):-s P250
argchoice:MDM10 (Protein):-s M10
argchoice:MDM20 (Protein):-s M20
argchoice:MDM40 (Protein):-s M40
argvalue:0

arg:NUMSHUF
argtype:slider
arglabel:# OF RANDOMIZED TRIALS
argmin:1
argmax:10000
argvalue:500

arg:ZED
arglabel:Statistical model
argtype:choice_menu
argchoice:no statistics calculated:-z -1
argchoice:raw mean & SD; don't correct for lib. length:-z 0
argchoice:-z1 wt. regression; correct for lib. length (default):-z 1
argchoice:-z2 max. likelihood of Lambda and K:-z 2
argchoice:-z3 Altschul-Gish parameters:-z 3
argchoice:-z 4:-z 4
argchoice:-z 5:-z 5
argchoice:-z 6 composition-based maximumlikelihood:-z 6
argchoice:-z 11 (-z1 regession against randomly-suffled seqs):-z 11
argchoice:-z 12 (-z2 regession against randomly-suffled seqs):-z 12
argchoice:-z 14 (-z4 regession against randomly-suffled seqs):-z 14
argchoice:-z 15 (-z5 regession against randomly-suffled seqs):-z 15
argchoice:-z 16 (-z6 regession against randomly-suffled seqs):-z 16
argvalue:2

arg:MARKX
arglabel:DISPLAY
argtype:choice_menu
argchoice:Identity="colon" Cons. repl.="." Mismatch=" ":-m 0
argchoice:Identity=" " Cons. repl.="x" Mismatch="X":-m 1
argchoice:Print only 1st seq; Identity="." Mismatch="residue":-m 2
argchoice:graph of conserved positions:-m 4
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


#------------------------------ SSEARCH  ( 5/14/08) ----------------------
item:SSEARCH - Pairwise Smith-Waterman (slow)
itemmethod:(sed "s/[#%]/>/"<in1 >in1.tmp; readseq -i1 -f8 in1.tmp -o=in1.seq1; readseq -i2 -f8 in1.tmp -o=in1.seq2; ssearch3 -k $NUMSHUF $MATRIX $ZED $MARKX -E $EVALUE in1.seq1 in1.seq2  > in1.out; $GDE_TEXTEDIT in1.out; rm in1*) &
itemhelp: doc/fasta/fasta.txt
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

arg:MATRIX
arglabel:SCORING MATRIX
argtype:choice_menu
argchoice:Default:
argchoice:DNA matrix (DNA default):-s $DAT/fasta/dna.mat
argchoice:Blosum50 (Protein default):-s BL50
argchoice:Blosum62 (Protein):-s BL62
argchoice:Blosum80 (Protein):-s BL80
argchoice:PAM120 (Protein):-s P120
argchoice:PAM250 (Protein):-s P250
argchoice:MDM10 (Protein):-s M10
argchoice:MDM20 (Protein):-s M20
argchoice:MDM40 (Protein):-s M40
argvalue:0

arg:NUMSHUF
argtype:slider
arglabel:# OF RANDOMIZED TRIALS
argmin:1
argmax:10000
argvalue:500

arg:ZED
arglabel:Statistical model
argtype:choice_menu
argchoice:no statistics calculated:-z -1
argchoice:raw mean & SD; don't correct for lib. length:-z 0
argchoice:-z1 wt. regression; correct for lib. length (default):-z 1
argchoice:-z2 max. likelihood of Lambda and K:-z 2
argchoice:-z3 Altschul-Gish parameters:-z 3
argchoice:-z 4:-z 4
argchoice:-z 5:-z 5
argchoice:-z 6 composition-based maximumlikelihood:-z 6
argchoice:-z 11 (-z1 regession against randomly-suffled seqs):-z 11
argchoice:-z 12 (-z2 regession against randomly-suffled seqs):-z 12
argchoice:-z 14 (-z4 regession against randomly-suffled seqs):-z 14
argchoice:-z 15 (-z5 regession against randomly-suffled seqs):-z 15
argchoice:-z 16 (-z6 regession against randomly-suffled seqs):-z 16
argvalue:2

arg:MARKX
arglabel:DISPLAY
argtype:choice_menu
argchoice:Identity="colon" Cons. repl.="." Mismatch=" ":-m 0
argchoice:Identity=" " Cons. repl.="x" Mismatch="X":-m 1
argchoice:Print only 1st seq; Identity="." Mismatch="residue":-m 2
argchoice:graph of conserved positions:-m 4
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


#------------------------- ALIGN  ( 2/28/05) ----------------------
item:ALIGN - Rigorous global alignment
itemmethod:(sed "s/[#%]/>/"<in1 >in1.tmp; readseq -i1 -f8 in1.tmp -o=in1.seq1; readseq -i2 -f8 in1.tmp -o=in1.seq2; $PROGRAM -w $RESPERLINE $MARKX $MATRIX in1.seq1 in1.seq2 > in1.out; fastaout.csh $MARKX in1.out; rm in1*)&
itemhelp: doc/fasta/align.txt
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

arg:PROGRAM
argtype:chooser
arglabel:Penalize gaps at ends of sequence?
argchoice:NO:align0
argchoice:YES:align
argvalue:0

arg:MATRIX
arglabel:SCORING MATRIX
argtype:choice_menu
argchoice:Default (Blosum50):
argchoice:DNA matrix (DNA default):-s $DAT/fasta2/dna.mat
argchoice:PAM120 (Protein):-s $DAT/fasta2/pam120.mat
argchoice:PAM250 (Protein):-s $DAT/fasta2/pam250.mat
argchoice:PAM250, Gonnet et al. (Protein):-s $DAT/fasta2/gonnet.mat
argchoice:Genetic Code Matrix (Protein):-s $DAT/fasta2/codaa.mat
argchoice:Weight Diagonals Only (Protein):-s $DAT/fasta2/altdiag.mat
argchoice:Lipman Alt.Matrix (Protein):-s $DAT/fasta2/altprot.mat
argchoice:Identity Matrix (Protein):-s $DAT/fasta2/idnaa.mat
argchoice:Weighted Identity Matrix (Protein):-s $DAT/fasta2/idpaa.mat
argvalue:0

arg:MARKX
arglabel:DISPLAY
argtype:choice_menu
argchoice:Identity="colon" Cons. repl.="." Mismatch=" ":-m 0
argchoice:Identity=" " Cons. repl.="x" Mismatch="X":-m 1
argchoice:Print only 1st seq; Identity="." Mismatch="residue":-m 2
argchoice:Read alignment into GDE:-m 3
argchoice:graph of conserved positions:-m 4
argvalue:0

arg:RESPERLINE
argtype:slider
arglabel:Nucs. or aa's printed per line
argmin:40
argmax:200
argvalue:60


#--------------- SHUFFLE - randomize sequences (11/26/06) -----------------
item:SHUFFLE - randomize sequences
itemmethod: sed "s/[#%]/>/" <in1 >in1.tmp; shuffle -s$SEED -w$WINDOW -o$OVERLAP <in1.tmp > in1.tmp2; btail.csh 3 in1.tmp2 in1.shuf; readseq -a -f2 -o=out1 in1.shuf; rm in1*
itemhelp: doc/xylem/shuffle.txt
itemopen:gde_help_viewer.csh

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

#-------------------------  D3HOM/D4HOM ( 2/ 8/05) --------------------------
item:DXHOM - Dot-matrix similarity (DNA)

# The directory fsapdoc must also be available in the $GDE_HELP_DIR,
# containing the file hom.asc from the FSAP package. Again, this
# directory can be implemented as a symbolic link.
itemmethod:readseq -i1 -fGenBank -o=in1.seq1 in1; readseq -i2 -fGenBank -o=in1.seq2 in1; hom.csh in1.seq1 $STRAND in1.seq2 in1.out $STARTX $FINISHX $STARTY $FINISHY $RANGE $MINPER $COMPFACT $KIND $LINESIZE $PROGRAM; ($GDE_TEXTEDIT in1.out; $RM_CMD in1*) &
itemhelp:doc/fsap/hom.txt
itemopen:gde_help_viewer.csh

arg:STARTX
argtype:slider
arglabel:STARTX
argmin:1
argmax:500000
argvalue:1

arg:FINISHX
argtype:slider
arglabel:FINISHX
argmin:1
argmax:500000
argvalue:500000

arg:STARTY
argtype:slider
arglabel:STARTY
argmin:1
argmax:500000
argvalue:1

arg:FINISHY
argtype:slider
arglabel:FINISHY
argmin:1
argmax:500000
argvalue:500000

arg:STRAND
arglabel:Which strand is X-axis?
argtype:chooser
argchoice:original:n
argchoice:opposite:y
argvalue:0

arg:PROGRAM
arglabel:K-tuple
argtype:chooser
argchoice:3:d3hom
argchoice:4:d4hom
argvalue:0

arg:RANGE
argtype:slider
arglabel:Dist. from center of window
argmin:1
argmax:30
argvalue:10

arg:MINPER
argtype:slider
arglabel:min. % similarity printed
argmin:40
argmax:100
argvalue:60

arg:COMPFACT
argtype:slider
arglabel:compression factor
argmin:1
argmax:500
argvalue:10

arg:KIND
argtype:chooser
argchoice:DNA:D
argchoice:RNA:R
argvalue:0

arg:LINESIZE
argtype:slider
arglabel:width (columns) of output line
argmin:40
argmax:150
argvalue:70

in:in1
informat:genbank
insave:

#-------------------------  P1HOM/P2HOM (11/ 5/00) --------------------------
item:PXHOM - Dot-matrix similarity (protein)

# The directory fsapdoc must also be available in the $GDE_HELP_DIR,
# containing the file hom.asc from the FSAP package. Again, this
# directory can be implemented as a symbolic link.
itemmethod:readseq -i1 -ffasta -o=in1.seq1 in1; readseq -i2 -ffasta -o=in1.seq2 in1; phom.csh in1.seq1 in1.seq2 in1.out $STARTX $FINISHX $STARTY $FINISHY $RANGE $MINPER $COMPFACT $LINESIZE $PROGRAM; ($GDE_TEXTEDIT in1.out; $RM_CMD in1*) &
itemhelp:doc/fsap/hom.asc
itemopen:gde_help_viewer.csh

arg:STARTX
argtype:slider
arglabel:STARTX
argmin:1
argmax:9000
argvalue:1

arg:FINISHX
argtype:slider
arglabel:FINISHX
argmin:1
argmax:9000
argvalue:9000

arg:STARTY
argtype:slider
arglabel:STARTY
argmin:1
argmax:9000
argvalue:1

arg:FINISHY
argtype:slider
arglabel:FINISHY
argmin:1
argmax:9000
argvalue:9000

arg:PROGRAM
arglabel:K-tuple
argtype:chooser
argchoice:1:p1hom
argchoice:2:p2hom
argvalue:0

arg:RANGE
argtype:slider
arglabel:Dist. from center of window
argmin:1
argmax:30
argvalue:10

arg:MINPER
argtype:slider
arglabel:min. % similarity printed
argmin:5
argmax:100
argvalue:30

arg:COMPFACT
argtype:slider
arglabel:compression factor
argmin:1
argmax:100
argvalue:10

arg:LINESIZE
argtype:slider
arglabel:width (columns) of output line
argmin:40
argmax:150
argvalue:70

in:in1
informat:genbank
insave:


############################## Database ##############################
menu:Database

#------------------- FINDKEY  (02/11/05)-----------------------
item:FINDKEY - Keyword Search
itemmethod: $KEYWORDS; (findkey $DATABASE in1.kw in1.nam in1.fnd; rm in1.kw; ($GDE_TEXTEDIT in1.fnd; rm in1.fnd)& ($GDE_TEXTEDIT in1.nam -geometry 25x50; rm in1.nam)&  )&
itemhelp:doc/xylem/findkey.txt
itemopen:gde_help_viewer.csh

arg:KEYWORDS
arglabel:KEYWORDS
argtype:chooser
argchoice:Single keyword:echo $KEY > in1.kw
argchoice:Create list of keywords:cat $DOC/xylem/GDE/keyfile.template > in1.tmp; $GDE_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: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
# As of GB114.0 RNA division is deleted from GenBank
#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
argvalue:0

arg:DBFILE
arglabel:Dataset name
argtype:text

in:in1
informat:flat

#------------------- FETCH ( 2/11/05) --------------------------
# 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:doc/xylem/fetch.txt
itemopen:gde_help_viewer.csh

arg:NAMES
arglabel:NAMES/ACCESSION #'S
argtype:chooser
argchoice:Single name/acc:echo $NAMEFILE > in1.nam
argchoice:Create list of names/acc#'s:cat $DOC/xylem/GDE/namefile.template > in1.tmpname; $GDE_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:PIR:-p
argchoice:PIR Dataset:-P $DBFILE
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:($GDE_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

#----------------  FEATURES - by feature key ( 2/16/07)  -------------------
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:doc/xylem/features.txt
itemopen:gde_help_viewer.csh

arg:FEALIST
arglabel:FEATURES TO EXTRACT
argtype:chooser
argchoice:Single feature:echo $FEAKEY > in1.feafile
argchoice:Create list of features:cat $DOC/xylem/GDE/feafile.template > in1.tmpfeafile; $GDE_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:operon:operon
argchoice:oriT:oriT
argchoice:polyA_signal:polyA_signal
argchoice:polyA_site:polyA_site
argchoice:precursor_RNA:precursor_RNA
argchoice:primer:primer
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:snoRNA:snoRNA
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 $DOC/xylem/GDE/names.template > in1.tmpefile; $GDE_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 $DOC/xylem/GDE/acc.template > in1.tmpefile; $GDE_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:2

arg:DBFILE
arglabel:Dataset name
argtype:text

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:GDE:sed -e 's/^>/#/' < in1.out >in1.result; (gde in1.result; rm in1.*)&
argchoice:Textedit windows:($GDE_TEXTEDIT in1.msg -geometry 50x25;rm in1.msg)& ($GDE_TEXTEDIT in1.exp -geometry 50x25; rm in1.exp) & ($GDE_TEXTEDIT in1.out -geometry 50x25;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


#--------------------  FEATURES - by expression (02/11/05)---------------------
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:doc/xylem/features.txt
itemopen:gde_help_viewer.csh

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 $DOC/xylem/GDE/expfile.template > in1.tmpexpfile; $GDE_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:sed -e 's/^>/#/' < in1.out >in1.result; (gde in1.result; rm in1.*)&
argchoice:Textedit windows:($GDE_TEXTEDIT in1.msg -geometry 50x25;rm in1.msg)& ($GDE_TEXTEDIT in1.out -geometry 50x25;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

#-------------- DBINST - Create DELILA Instructions ( 4/ 8/94)  --------------
item:DBINST - GenBank feature --> DELILA Instruct.
# sed corrects errors in GDE-generated genbank output
itemmethod:(mkdir in1.dir; sed -e "s/^LOCUS */LOCUS       /" -e "s/^  ORGANISM/ORGANISM  /" -e "s/^ ACCESSION/ACCESSION /" -e "/^$/d"  in1 > in1.dir/db; cd in1.dir; dbinst.csh $FEAKEY $FROM $TO $REMDUP $ALLOWP $ALSHIFT >dbinstp; dbinst; mv $REFPOINTinst ../in1.$REFPOINTinst; cd ..; rm -r in1.dir; ($GDE_TEXTEDIT in1.$REFPOINTinst; rm in1.$REFPOINTinst)& ) &
itemhelp:doc/delila/dbinst.asc
itemopen:gde_help_viewer.csh

arg:FEAKEY
arglabel: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:REFPOINT
arglabel:REFERENCE POINT
argtype:chooser
argchoice:Beginning:b
argchoice:End:e
argchoice:Whole object:o
argchoice:Space between objects:s
argvalue:0

arg:FROM
arglabel:start   upstream   from reference point
argtype:slider
argmin:-100
argmax:100
argvalue:-20

arg:TO
arglabel:finish downstream from reference point
argtype:slider
argmin:-100
argmax:100
argvalue:20

arg:REMDUP
arglabel:REMOVE DUPLICATED INSTRUCTIONS?
argtype:chooser
argchoice:Yes:r
argchoice:No:n
argvalue:0

arg:ALLOWP
arglabel:ALLOW PARTIAL OBJECTS?
argtype:chooser
argchoice:Yes:f
argchoice:No:n
argvalue:0

arg:ALSHIFT
arglabel:ALIGNMENT SHIFT FOR 0 BASE
argtype:slider
argmin:-100
argmax:100
argvalue:0

in:in1
informat:genbank
insave:

#--------- DELILA - Retrieve seq. using DELILA Instr. ( 4/ 8/94)  ------------
#    Required DELILA programs:  dbbk catal delila bk2seq
item:DELILA - DELILA Instruct --> sequence
itemmethod:(mkdir in1.dir; $DATABASE; cd in1.dir; dbbk; echo "n" >catalp; echo -n "" >l2; echo -n "" >l3; catal; $INSTFILE; delila; mv listing ../in1.listing; mv book ../in1.book; mv changes ../in1.changes; cd ..; rm -r in1.dir; ($GDE_TEXTEDIT in1.changes; rm in1.changes)& ($GDE_TEXTEDIT in1.listing; rm in1.listing)&  $WHERE) &
itemhelp:doc/delila/delila.asc
itemopen:gde_help_viewer.csh

arg:INSTFILE
argtype:chooser
arglabel:DELILA INSTRUCTIONS
argchoice:Paste from $GDE_TEXTEDIT window:cp $DAT/delila/inst.template inst; $GDE_TEXTEDIT inst
argchoice:Read from file:cp $FNAME inst
argvalue:0

arg:FNAME
argtype:text
arglabel:DELILA instruction filename (.inst)

# sed corrects errors in GDE-generated genbank output
arg:DATABASE
arglabel:DATABASE
argtype:chooser
argchoice:GenBank file:cp $DBFILE in1.dir/db
# This item won't work until GDE is fixed to correct some problems
# with generation of GenBank files.
#argchoice:Selected sequences:sed -e "s/^LOCUS */LOCUS       /"  -e "s/^ ACCESSION/ACCESSION /" -e "/^$/d"  in1 > in1.dir/db
argvalue:0

arg:DBFILE
arglabel:GenBank file (.gen)
argtype:text

arg:WHERE
arglabel:WHERE TO SENT OUTPUT
argtype:chooser
argchoice:GDE:mv in1.book book; echo -n "" > inst; bk2seq; tail +5 protseq | sed -e "s/* /#/" -e "s/\.//" >in1.flat; (gde in1.flat;rm in1.flat)&
argchoice:Textedit windows:($GDE_TEXTEDIT in1.book; rm in1.book )&
argvalue:0

in:in1
informat:genbank
insave:

#-------------------------- blastp  ( 2/10/05) ----------------------
# Performs remote BLAST search at NCBI using blastcl3 

item:NCBI BLASTP - remote protein database search
itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta; nice -n 10 blastcl3 -i in1.fasta -p blastp -d $DBASE $RESTRICT -M $MATRIX -Q $GENCODE  -D $GENCODE -g $GAPPED -e $EVALUE -m $VOPTIONS  > in1.blastp; python $BIRCH/script/dbsout.py in1.blastp $WHERE; rm in1*) &
itemhelp: doc/NCBI/netblast/netblast.txt
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

#See http://www.ncbi.nlm.nih.gov/blast/html/blastcgihelp.html#protein_databases
arg:DBASE
argtype:choice_menu
arglabel:Database
argchoice:SwissProt:swissprot
argchoice:GenBank NonRedundant (Protein):nr
argchoice:Escherichia coli:ecoli
argchoice:Saccharomyces cerevisiae:yeast
argchoice:GenBank Patented:pat
argchoice:PDB - Brookhaven 3D:pdb
argvalue:0

arg:RESTRICT
arglabel:Restrict search to entries containing string:
argtype:chooser
argchoice:Yes:-u $SSTRING
argchoice:No:
argvalue:1

arg:SSTRING
arglabel:Search string
argtype:text
argtext:

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

#-------------------------- blastn  ( 2/10/05) ----------------------
# Performs remote BLAST search at NCBI using blastcl3

item:NCBI BLASTN - DNA vs. remote DNA database
itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta; nice -n 10 blastcl3 -i in1.fasta -p blastn -d $DBASE $RESTRICT -S $STRANDS -g $GAPPED -e $EVALUE -m $VOPTIONS  > in1.blastn; python $BIRCH/script/dbsout.py in1.blastn $WHERE; rm in1*) &
itemhelp: doc/NCBI/netblast/netblast.txt
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

# See http://www.ncbi.nlm.nih.gov/blast/html/blastcgihelp.html#protein_databases
arg:DBASE
argtype:choice_menu
arglabel:Database
argchoice:GenBank NonRedundant:nr
argchoice:GenBank EST:est
argchoice:GenBank EST Human:est_human
argchoice:GenBank EST Mouse:est_mouse
argchoice:GenBank EST Other:est_others
argchoice:GenBank Genome Survey Seq.:gss
argchoice:GenBank High-Throughput genomic:htgs
argchoice:GenBank Patented:pat
argchoice:GenBank Saccharomyces cerevisiae:yeast
argchoice:GenBank Mitochondrial:mito
argchoice:GenBank Vector:vector
argchoice:GenBank E. coli:ecoli
argchoice:GenBank Seq.-Tagged Sites:dbsts
argvalue:0

arg:RESTRICT
arglabel:Restrict search to entries containing string:
argtype:chooser
argchoice:Yes:-u $SSTRING
argchoice:No:
argvalue:1

arg:SSTRING
arglabel:Search string
argtype:text
argtext:

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

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

#-------------------------- blastx  ( 2/10/05) ----------------------
# Performs remote BLAST search at NCBI using blastcl3

item:NCBI BLASTX - trans. DNA vs remote protein database
itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta; nice -n 10 blastcl3 -i in1.fasta -p blastx -d $DBASE $RESTRICT -M $MATRIX -Q $GENCODE  -D $GENCODE -g $GAPPED -e $EVALUE -m $VOPTIONS  > in1.blastx; python $BIRCH/script/dbsout.py in1.blastx $WHERE; rm in1*) &
itemhelp: doc/NCBI/netblast/netblast.txt
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

#See http://www.ncbi.nlm.nih.gov/blast/html/blastcgihelp.html#protein_databases
arg:DBASE
argtype:choice_menu
arglabel:Database
argchoice:SwissProt:swissprot
argchoice:GenBank NonRedundant (Protein):nr
argchoice:Escherichia coli:ecoli
argchoice:Saccharomyces cerevisiae:yeast
argchoice:GenBank Patented:pat
argchoice:PDB - Brookhaven 3D:pdb
argvalue:0

arg:RESTRICT
arglabel:Restrict search to entries containing string:
argtype:chooser
argchoice:Yes:-u $SSTRING
argchoice:No:
argvalue:1

arg:SSTRING
arglabel:Search string
argtype:text
argtext:

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

#-------------------------- tblastn  ( 2/10/05) ----------------------
# Performs remote BLAST search at NCBI using blastcl3

item:NCBI TBLASTN - protein vs. remote trans. DNA database
itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta; nice -n 10 blastcl3 -i in1.fasta -p tblastn -d $DBASE $RESTRICT -g $GAPPED -e $EVALUE -m $VOPTIONS  > in1.tblastn; python $BIRCH/script/dbsout.py in1.tblastn $WHERE; rm in1*) &
itemhelp: doc/NCBI/netblast/netblast.txt
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

# See http://www.ncbi.nlm.nih.gov/blast/html/blastcgihelp.html#protein_databases
arg:DBASE
argtype:choice_menu
arglabel:Database
argchoice:GenBank NonRedundant:nr
argchoice:GenBank EST:est
argchoice:GenBank EST Human:est_human
argchoice:GenBank EST Mouse:est_mouse
argchoice:GenBank EST Other:est_others
argchoice:GenBank Genome Survey Seq.:gss
argchoice:GenBank High-Throughput genomic:htgs
argchoice:GenBank Patented:pat
argchoice:GenBank Saccharomyces cerevisiae:yeast
argchoice:GenBank Mitochondrial:mito
argchoice:GenBank Vector:vector
argchoice:GenBank E. coli:ecoli
argchoice:GenBank Seq.-Tagged Sites:dbsts
argvalue:0

arg:RESTRICT
arglabel:Restrict search to entries containing string:
argtype:chooser
argchoice:Yes:-u $SSTRING
argchoice:No:
argvalue:1
 
arg:SSTRING
arglabel:Search string
argtype:text
argtext:

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

#-------------------------- tblastx  ( 2/10/05) ----------------------
# Performs remote BLAST search at NCBI using blastcl3

item:NCBI TBLASTX - trans. DNA vs. remote trans. DNA database
itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta; nice -n 10 blastcl3 -i in1.fasta -p tblastn -d $DBASE $RESTRICT -g $GAPPED -e $EVALUE -m $VOPTIONS  > in1.tblastn; python $BIRCH/script/dbsout.py in1.tblastn $WHERE; rm in1*) &
itemhelp: doc/NCBI/netblast/netblast.txt
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

# See http://www.ncbi.nlm.nih.gov/blast/html/blastcgihelp.html#protein_databases
arg:DBASE
argtype:choice_menu
arglabel:Database
argchoice:GenBank NonRedundant:nr
argchoice:GenBank EST:est
argchoice:GenBank EST Human:est_human
argchoice:GenBank EST Mouse:est_mouse
argchoice:GenBank EST Other:est_others
argchoice:GenBank Genome Survey Seq.:gss
argchoice:GenBank High-Throughput genomic:htgs
argchoice:GenBank Patented:pat
argchoice:GenBank Saccharomyces cerevisiae:yeast
argchoice:GenBank Mitochondrial:mito
argchoice:GenBank Vector:vector
argchoice:GenBank E. coli:ecoli
argchoice:GenBank Seq.-Tagged Sites:dbsts
argvalue:0

arg:RESTRICT
arglabel:Restrict search to entries containing string:
argtype:chooser
argchoice:Yes:-u $SSTRING
argchoice:No:
argvalue:1
 
arg:SSTRING
arglabel:Search string
argtype:text
argtext:

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

#----------------------- FASTA (DNA/RNA) ( 4/10/06) ----------------------
item:FASTA (DNA/RNA vs. DNA database)
itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta; nice -n 10 $PROGRAM -Q -n -b $NUMOFSCORES -d $NUMOFALN  $MARKX $ZED -E $EVALUE in1.fasta $DBASE $KTUP > in1.out; python $birch/script/dbsout.py in1.out $WHERE; rm in1.fasta in1) &
itemhelp: doc/fasta/fasta.txt
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

arg:DBASE
argtype:choice_menu
arglabel:Database
argchoice:GenBank Primate:@$DAT/fasta/gbpri.fil
argchoice:GenBank Rodent:@$DAT/fasta/gbrod.fil
argchoice:GenBank all Mammal:@$DAT/fasta/gbmam.fil
argchoice:GenBank verteBrates:@$DAT/fasta/gbvrt.fil
argchoice:GenBank Inverts:@$DAT/fasta/gbinv.fil
argchoice:GenBank pLants:@$DAT/fasta/gbpln.fil
argchoice:GenBank Expressed Sequence Tags:@$DAT/fasta/gbest.fil
argchoice:GenBank phaGe:@$DAT/fasta/gbphg.fil
argchoice:GenBank bacTeria:@$DAT/fasta/gbbct.fil
argchoice:GenBank sYnthetic:@$DAT/fasta/gbsyn.fil
argchoice:GenBank Viral:@$DAT/fasta/gbvrl.fil
argchoice:GenBank Unannotated:@$DAT/fasta/gbuna.fil
argchoice:GenBank Patented:@$DAT/fasta/gbpat.fil
argchoice:GenBank Seq. Tagged Sites:@$DAT/fasta/gbsts.fil
argchoice:GenBank High Throughput Genomic:@$DAT/fasta/gbhtg.fil
argchoice:GenBank Genome Survey Seq.:@$DAT/fasta/gbgss.fil
argchoice:GenBank All divisions (VERY Long!):@$DAT/fasta/genbank.fil
argchoice:User-created file (FASTA format):$USERFILE

arg:USERFILE
arglabel:filename
argtype:text

arg:PROGRAM
arglabel:PROGRAM
argtype:choice_menu
argchoice:fasta - quick, sensitive:fasta3
argchoice:ssearch - SLOW!, exhaustive:ssearch3
argvalue:0

arg:KTUP
argtype:slider
arglabel:K-TUPLE
argmin:1
argmax:6
argvalue:4

arg:MARKX
arglabel:DISPLAY
argtype:choice_menu
argchoice:Identity="colon" Cons. repl.="." Mismatch=" ":-m 0
argchoice:Identity=" " Cons. repl.="x" Mismatch="X":-m 1
argchoice:Print only 1st seq; Identity="." Mismatch="residue":-m 2
argchoice:graph of conserved positions:-m 4
argvalue:0

arg:ZED
arglabel:Statistical model
argtype:choice_menu
argchoice:no statistics calculated:-z -1
argchoice:raw mean & SD; don't correct for lib. length:-z 0
argchoice:wt. regression; correct for lib. length (default):-z 1
argchoice:max. likelihood of Lambda and K:-z 2
argchoice:Altschul-Gish parameters:-z 3
argchoice:-z 4:-z 4
argchoice:-z 5:-z 5
argchoice:-z 11 (most seqs. closely-related):-z 11
argchoice:-z 12 (most seqs. closely-related):-z 12
argchoice:-z 14 (most seqs. closely-related):-z 14
argchoice:-z 15 (most seqs. closely-related):-z 15
argvalue:2

arg:NUMOFSCORES
argtype:slider
arglabel:Number of Best Scores to Report
argmin:1
argmax:1000
argvalue:20

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

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

#-------------------------- fasta (protein)  ( 4/10/06) ----------------------
item:FASTA (protein vs. protein database)
itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta;nice -n 10 $PROGRAM -Q -d $NUMOFALN $MARKX $MATRIX $ZED -E $EVALUE in1.fasta $DBASE $KTUP > in1.out; python $birch/script/dbsout.py in1.out $WHERE; rm in1*) &
itemhelp: doc/fasta/fasta.txt
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

arg:DBASE
argtype:choice_menu
arglabel:Database
argchoice:PIR:@$DAT/fasta/pir.fil
argchoice:GenPept:$GENPEPT/genpept.wrp
argchoice:User-created file (FASTA format):$USERFILE

arg:USERFILE
arglabel:filename
argtype:text

arg:PROGRAM
arglabel:PROGRAM
argtype:choice_menu
argchoice:fasta - (quick, sensitive):fasta3
argchoice:ssearch - (SLOW!, exhaustive):ssearch3
argvalue:0

arg:KTUP
argtype:slider
arglabel:K-TUPLE
argmin:1
argmax:2
argvalue:2

arg:MATRIX
arglabel:SCORING MATRIX
argtype:choice_menu
argchoice:Blosum50 (Protein default):-s BL50
argchoice:Blosum62 (Protein):-s BL62
argchoice:Blosum80 (Protein):-s BL80
argchoice:PAM120 (Protein):-s P120
argchoice:PAM250 (Protein):-s P250
argchoice:MDM10 (Protein):-s M10
argchoice:MDM20 (Protein):-s M20
argchoice:MDM40 (Protein):-s M40
argvalue:0

arg:ZED
arglabel:Statistical model
argtype:choice_menu
argchoice:no statistics calculated:-z -1
argchoice:raw mean & SD; don't correct for lib. length:-z 0
argchoice:wt. regression; correct for lib. length (default):-z 1
argchoice:max. likelihood of Lambda and K:-z 2
argchoice:Altschul-Gish parameters:-z 3
argchoice:-z 4:-z 4
argchoice:-z 5:-z 5
argchoice:-z 11 (most seqs. closely-related):-z 11
argchoice:-z 12 (most seqs. closely-related):-z 12
argchoice:-z 14 (most seqs. closely-related):-z 14
argchoice:-z 15 (most seqs. closely-related):-z 15
argvalue:2

arg:SCALESCORES
arglabel:Scale scores by ln(Nquery)/ln(Nlibrary)
argtype:chooser
argchoice:Yes (weights short similarities):-e
argchoice:No:
argvalue:1

arg:MARKX
arglabel:DISPLAY
argtype:choice_menu
argchoice:Identity="colon" Cons. repl.="." Mismatch=" ":-m 0
argchoice:Identity=" " Cons. repl.="x" Mismatch="X":-m 1
argchoice:Print only 1st seq; Identity="." Mismatch="residue":-m 2
argchoice:graph of conserved positions:-m 4
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:NUMOFALN
argtype:slider
arglabel:Number of Alignments to Report
argmin:1
argmax:100
argvalue:20

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

#-------------------------- fastx/y (protein)   4/10/06) ----------------------
item:FASTA (cDNA vs. protein database)
itemmethod:(sed "s/[#%]/>/"<in1 >in1.fasta;nice -n 10 $PROGRAM -Q -d $NUMOFALN $MARKX $MATRIX $ZED -E $EVALUE in1.fasta $DBASE $KTUP > in1.out; python $birch/script/dbsout.py in1.out $WHERE; rm in1*) &
itemhelp: doc/fasta/fasta.txt
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

arg:DBASE
argtype:choice_menu
arglabel:Database
argchoice:PIR:@$DAT/fasta/pir.fil
argchoice:GenPept:$GENPEPT/genpept.wrp
argchoice:User-created file (FASTA format):$USERFILE

arg:USERFILE
arglabel:filename
argtype:text

arg:PROGRAM
arglabel:Allow gaps
argtype:choice_menu
argchoice:fastx - between codons only (faster):fastx3
argchoice:fasty - WITHIN codons (sensitive):fasty3
argvalue:0

arg:KTUP
argtype:slider
arglabel:K-TUPLE
argmin:1
argmax:2
argvalue:2

arg:MATRIX
arglabel:SCORING MATRIX
argtype:choice_menu
argchoice:Blosum50 (Protein default):-s BL50
argchoice:Blosum62 (Protein):-s BL62
argchoice:Blosum80 (Protein):-s BL80
argchoice:PAM120 (Protein):-s P120
argchoice:PAM250 (Protein):-s P250
argchoice:MDM10 (Protein):-s M10
argchoice:MDM20 (Protein):-s M20
argchoice:MDM40 (Protein):-s M40
argvalue:0

arg:ZED
arglabel:Statistical model
argtype:choice_menu
argchoice:no statistics calculated:-z -1
argchoice:raw mean & SD; don't correct for lib. length:-z 0
argchoice:wt. regression; correct for lib. length (default):-z 1
argchoice:max. likelihood of Lambda and K:-z 2
argchoice:Altschul-Gish parameters:-z 3
argchoice:-z 4:-z 4
argchoice:-z 5:-z 5
argchoice:-z 11 (most seqs. closely-related):-z 11
argchoice:-z 12 (most seqs. closely-related):-z 12
argchoice:-z 14 (most seqs. closely-related):-z 14
argchoice:-z 15 (most seqs. closely-related):-z 15
argvalue:2

arg:SCALESCORES
arglabel:Scale scores by ln(Nquery)/ln(Nlibrary)
argtype:chooser
argchoice:Yes (weights short similarities):-e
argchoice:No:
argvalue:1

arg:MARKX
arglabel:DISPLAY
argtype:choice_menu
argchoice:Identity="colon" Cons. repl.="." Mismatch=" ":-m 0
argchoice:Identity=" " Cons. repl.="x" Mismatch="X":-m 1
argchoice:Print only 1st seq; Identity="." Mismatch="residue":-m 2
argchoice:graph of conserved positions:-m 4
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:NUMOFALN
argtype:slider
arglabel:Number of Alignments to Report
argmin:1
argmax:100
argvalue:20

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

#----------------------- tfasta (protein) ( 4/10/06) -----------------------
item:TFASTA (Protein vs. DNA Database, Translated in 6 Reading Frames)
itemmethod:(sed -e "s/[#%]/>/"<in1 >in1.tfasta; nice -n 10 $PROGRAM -Q -d $NUMOFALN $MARKX $MATRIX $ZED -E $EVALUE in1.tfasta $DBASE $KTUP $FRAMES > in1.out; python $birch/script/dbsout.py in1.out $WHERE; rm in1*) &
itemhelp: doc/fasta/fasta.txt
itemopen:gde_help_viewer.csh

in:in1
informat:flat
insave:

arg:DBASE
argtype:choice_menu
arglabel:Database
argchoice:GenBank Primate:@$DAT/fasta/gbpri.fil
argchoice:GenBank Rodent:@$DAT/fasta/gbrod.fil
argchoice:GenBank all Mammal:@$DAT/fasta/gbmam.fil
argchoice:GenBank verteBrates:@$DAT/fasta/gbvrt.fil
argchoice:GenBank Inverts:@$DAT/fasta/gbinv.fil
argchoice:GenBank pLants:@$DAT/fasta/gbpln.fil
argchoice:GenBank Expressed Sequence Tags:@$DAT/fasta/gbest.fil
argchoice:GenBank phaGe:@$DAT/fasta/gbphg.fil
argchoice:GenBank bacTeria:@$DAT/fasta/gbbct.fil
argchoice:GenBank sYnthetic:@$DAT/fasta/gbsyn.fil
argchoice:GenBank Viral:@$DAT/fasta/gbvrl.fil
argchoice:GenBank Unannotated:@$DAT/fasta/gbuna.fil
argchoice:GenBank Patented:@$DAT/fasta/gbpat.fil
argchoice:GenBank Seq. Tagged Sites:@$DAT/fasta/gbsts.fil
argchoice:GenBank High Throughput Genomic:@$DAT/fasta/gbhtg.fil
argchoice:GenBank Genome Survey Seq.:@$DAT/fasta/gbgss.fil
argchoice:GenBank All divisions (VERY Long!):@$DAT/fasta/genbank.fil
argchoice:User-created file (FASTA format):$USERFILE

arg:USERFILE
arglabel:filename
argtype:text

arg:PROGRAM
arglabel:Allow gaps
argtype:choice_menu
argchoice:tfasta - none:tfasta3
argchoice:tfastx - between codons only (faster):tfastx3
argchoice:tfasty - WITHIN codons (sensitive):tfasty3
argvalue:0

arg:FRAMES
arglabel:Translate
argtype:chooser
argchoice:3 frames:-3
argchoice:6 frames:
argvalue:1

arg:KTUP
argtype:slider
arglabel:K-TUPLE
argmin:1
argmax:2
argvalue:2

arg:MATRIX
arglabel:SCORING MATRIX
argtype:choice_menu
argchoice:Blosum50 (Protein default):-s BL50
argchoice:Blosum62 (Protein):-s BL62
argchoice:Blosum80 (Protein):-s BL80
argchoice:PAM120 (Protein):-s P120
argchoice:PAM250 (Protein):-s P250
argchoice:MDM10 (Protein):-s M10
argchoice:MDM20 (Protein):-s M20
argchoice:MDM40 (Protein):-s M40
argvalue:0

arg:SCALESCORES
arglabel:Scale scores by ln(Nquery)/ln(Nlibrary)
argtype:chooser
argchoice:Yes (weights short similarities):-e
argchoice:No:
argvalue:1

arg:MARKX
arglabel:DISPLAY
argtype:choice_menu
argchoice:Identity="colon" Cons. repl.="." Mismatch=" ":-m 0
argchoice:Identity=" " Cons. repl.="x" Mismatch="X":-m 1
argchoice:Print only 1st seq; Identity="." Mismatch="residue":-m 2
argchoice:graph of conserved positions:-m 4
argvalue:0

arg:ZED
arglabel:Statistical model
argtype:choice_menu
argchoice:no statistics calculated:-z -1
argchoice:raw mean & SD; don't correct for lib. length:-z 0
argchoice:wt. regression; correct for lib. length (default):-z 1
argchoice:max. likelihood of Lambda and K:-z 2
argchoice:Altschul-Gish parameters:-z 3
argchoice:-z 4:-z 4
argchoice:-z 5:-z 5
argchoice:-z 11 (most seqs. closely-related):-z 11
argchoice:-z 12 (most seqs. closely-related):-z 12
argchoice:-z 14 (most seqs. closely-related):-z 14
argchoice:-z 15 (most seqs. closely-related):-z 15
argvalue:2

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

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


############################## Patterns ##############################
menu:Patterns

#------------------------- TESTCODE ( 2/ 8/05) --------------------------
item:Testcode - find protein coding sequences

# The directory fsapdoc must be available in the $GDE_HELP_DIR,
# containing the file testcode.asc from the FSAP package. Again, this
# directory can be implemented as a symbolic link.
itemmethod:testcode.csh in1 in1.out $START $FINISH $WHICH $FORMAT $WINDOW $SKIP;($GDE_TEXTEDIT in1.out; $RM_CMD in1*) &
itemhelp:doc/fsap/testcode.txt
itemopen:gde_help_viewer.csh

arg:START
argtype:slider
arglabel:START
argmin:1
argmax:500000
argvalue:1

arg:FINISH
argtype:slider
arglabel:FINISH
argmin:1
argmax:500000
argvalue:500000

arg:WHICH
arglabel:Which strand?
argtype:chooser
argchoice:original:i
argchoice:opposite:o
argvalue:0

arg:FORMAT
arglabel:Output format
argtype:chooser
argchoice:Histogram:g
argchoice:Table:t
argvalue:0

arg:WINDOW
argtype:slider
arglabel:# codons in search window
argmin:10
argmax:200
argvalue:67

arg:SKIP
argtype:slider
arglabel:# to skip for each window
argmin:1
argmax:200
argvalue:10

in:in1
informat:genbank
insave:

#------------------------- TACG (03/05/2005) --------------------------
item:TACG - pattern searching (Version 3.6)

#itemmethod: (readseq -fgb -o=in1.tmp in1; python $BIRCH/script/tacg.py $TOPOLOGY $DEGENERACY $MATFILE $PTRNSW -w $WIDTH $CUTS $LAMAP $LIMAP $TRANS $STRANDS $REXPSW $REXP --pdf $ADDITIONAL in1.tmp in1.out in1.pdf; $RM_CMD in1 in1.tmp; ($GDE_TEXTEDIT in1.out; $RM_CMD in1.out)& if [ -f in1.pdf ]; then ($GDE_PDFVIEW in1.pdf; $RM_CMD in1.pdf)& fi)&
itemmethod: (readseq -fgb -o=in1.tmp in1; python $BIRCH/script/tacg.py $TOPOLOGY $DEGENERACY $MATFILE $PTRNSW -w $WIDTH $CUTS $LAMAP $LIMAP $TRANS $STRANDS -H --pdf  in1.tmp in1.html in1.pdf; $RM_CMD in1 in1.tmp; (browser.csh file://$PWD/in1.html)&  if [ -f in1.pdf ]; then ($GDE_PDFVIEW in1.pdf; $RM_CMD in1.pdf in1.html)& fi)&

itemhelp:doc/tacg/tacg.man.txt
itemopen:gde_help_viewer.csh

arg:TOPOLOGY
argtype:chooser
arglabel:Topology
argchoice:Linear:-f1
argchoice:Circular:-f0
argvalue:0

arg:DEGENERACY
argtype:choice_menu
arglabel:Degeneracy in input sequence
argchoice:none - only agctu:-D 0
argchoice:fastsearch in nondegen regions; slow in degen regions:-D 1
argchoice:degens OK; ignore in KEY, match outside KEY:-D 2
argchoice:degens OK; expand in KEY, find EXACT matches:-D 3
argchoice:degens OK; expand in KEY, find all possible matches:-D 4
argvalue:0

arg:PTRNSW
argtype:chooser
arglabel:SEARCH FOR A PATTERN
argchoice:Yes:-p $PTRN
argchoice:No:
argvalue:1

arg:PTRN
argtype:text
arglabel:type pattern here eg. Pit1,tatwcata,1
argtext: 

arg:MATFILE
argtype:choice_menu
arglabel:SEARCH FOR TRANSCRIPTION FACTOR BINDING SITES
argchoice:none (default):
argchoice:full TRANSFAC database:-R $DAT/tacg/matrix.dat.FULL.1998 -#$MATCUTOFF $MATNAMES
argchoice:yeast transcription factor sites:-R $DAT/tacg/matrix.data.yeast -#$MATCUTOFF $MATNAMES
argvalue:0

arg:MATCUTOFF
argtype:slider
arglabel:percent match required for transcription sites
argmin:50
argmax:100
argvalue:100

arg:MATNAMES
argtype:chooser
arglabel:Limit search to specific sites?
argchoice:Yes:-x $NAMELIST
argchoice:No:
argvalue:1

arg:NAMELIST
argtype:text
arglabel:names of sites to search for eg. rCAR1,ABF1
argtext: 

#arg:REXPRULE
#argtype:chooser
#arglabel:SEARCH FOR
#argchoice:none:
#argchoice:REGULAR EXPRESSIONS:-r /'FILE:$RFILE/'
#argchoice:RULES:--rulefile $RFILE -R $PFILE
#argvalue:0

#arg:RFILE
#argtype:text
#arglabel:filename for reg. exp. or rules
#argtext: 

#arg:PFILE
#argtype:text
#arglabel:filename for patterns
#argtext: 

arg:CUTS
argtype:chooser
arglabel:print cut sites in tabular form
argchoice:Yes:-s
argchoice:No:
argvalue:0

arg:LAMAP
argtype:chooser
arglabel:LADDER MAP?
argchoice:Yes:-l
argchoice:No:
argvalue:1

arg:LIMAP
argtype:chooser
arglabel:PRINT SEQUENCE AND SITES?
argchoice:Yes:-L
argchoice:No:
argvalue:1

arg:STRANDS
argtype:chooser
arglabel:Strands
argchoice:one:--strands 1
argchoice:two:--strands 2
argvalue:0

arg:TRANS
argtype:choice_menu
arglabel:translation to accompany sequence
argchoice:none:
argchoice:1 frame, 1-letter code:-T1,1
argchoice:3 frames, 1-letter code:-T3,1
argchoice:6 frames, 1-letter code:-T6,1
argchoice:1 frame, 3-letter code:-T1,3
argchoice:3 frames, 3-letter code:-T3,3
argchoice:6 frames, 3-letter code:-T6,3
argvalue:0

arg:GC
argtype:choice_menu
arglabel:Genetic Code for translation
argchoice:Universal:-C0
argchoice:Vert. mitochondrial:-C1
argchoice:S. cerivisiae mitochondrial:-C2
argchoice:N. crassa mitochondrial:-C3
argchoice:Invertebrate mitochondrial:-C4
argchoice:Ciliate mitochondrial:-C5
argchoice:Euplotid mitochondrial:-C6
argchoice:Euplotid nuclear:-C7
argchoice:Bacterial:-C8
argchoice:Alt. Yeast:-C9
argchoice:Ascidian mitochondrial:-C10
argchoice:Flatworm:-C11
argchoice:Blepharisma:-C12
argvalue:0


arg:WIDTH
argtype:slider
arglabel:OUTPUT WIDTH (bp/line)
argmin:60
argmax:210
argvalue:60

in:in1
informat:genbank
insave:


############################## Alignment ##############################
menu:Alignment

#-------------------- clustalx 1.82 (11/25/03) --------------------------
#

item:clustalx
#itemmethod:(tr "~" "-" <in1 | readseq -a -p -f=PEARSON | sed "s/:.*//" |sed "s/\*//" > in1.wrp; clustalx in1.wrp; rm in1 in1.wrp)&
itemmethod:(tr "~" "-" <in1 | readseq -a -p -f=PEARSON | sed "s/\*//" > in1.wrp; clustalx in1.wrp; rm in1 in1.wrp)&
itemhelp:doc/clustalx/clustalx_help
itemopen:gde_help_viewer.csh


in:in1
informat:genbank
insave:


#-------------------- TCOFFEE 1.37 ( 3/ 2/05) --------------------------
#

item:TCOFFEE - multiple alignment
itemmethod:(tr "~" "-" <in1 | readseq -a -p -f=PEARSON | sed "s/\*//" > in1.fsa; $RM_CMD in1; t_coffee in1.fsa $MATRIX -ktuple=$KTUP -do_normalise=$NORMALIZE -extend=$EXTEND -gapopen=$GAPOPEN -gapext=$GAPEXT -cosmetic_penalty=$COSPEN -tg_mode=$TGMODE -dp_mode=$DPMODE -ndiag=$NDIAG -diag_mode=$DIAGMODE -tree_mode=$TREEMODE -output=msf_aln,score_html -outorder=aligned; $WHERE)&
itemhelp:doc/tcoffee/t_coffee_doc.html
itemopen:gde_help_viewer.csh

arg:MATRIX
arglabel:substitution matrix
argtype:choice_menu
argchoice:default:
argchoice:blosum30mt:-in=Xblosum30mt
argchoice:blosum40mt:-in=Xblosum40mt
argchoice:blosum45mt:-in=Xblosum45mt
argchoice:blosum55mt:-in=Xblosum55mt
argchoice:blosum62mt:-in=Xblosum62mt
argchoice:blosum62mt2:-in=Xblosum62mt2
argchoice:blosum80mt:-in=Xblosum80mt
argchoice:pam120mt:-in=Xpam120mt
argchoice:pam160mt:-in=Xpam160mt
argchoice:pam250mt:-in=Xpam250mt
argchoice:pam350mt:-in=Xpam350mt
argchoice:md_40mt:-in=Xmd_40mt
argchoice:md_120mt:-in=Xmd_120mt
argchoice:md_250mt:-in=Xmd_250mt
argchoice:md_350mt:-in=Xmd_350mt
argchoice:idmat:-in=Xidmat
argchoice:est_idmat:-in=Xest_idmat
argchoice:coil_mat:-in=Xcoil_mat
argchoice:alpha_mat:-in=Xalpha_mat
argchoice:beta_mat:-in=Xbeta_mat
argchoice:rblosum30mt:-in=Xrblosum30mt
argchoice:rblosum62mt:-in=Xrblosum62mt
argchoice:rblosum80mt:-in=Xrblosum80mt
argchoice:rpam120mt:-in=Xrpam120mt
argchoice:rpam160mt:-in=Xrpam160mt
argchoice:rpam250mt:-in=Xrpam250mt
argchoice:rpam350mt:-in=Xrpam350mt
argchoice:ralpha_mat:-in=Xralpha_mat
argchoice:rbeta_mat:-in=Xrbeta_mat
argchoice:rcoil_mat:-in=Xrcoil_mat
argchoice:tmpam250mt:-in=Xtmpam250mt
argchoice:rtmpam250mt:-in=Xrtmpam250mt
argvalue:0


arg:KTUP
argtype:slider
arglabel:K-TUPLE
argmin:1
argmax:4
argvalue:2

arg:DPMODE
arglabel:Dynamic programming mode
argtype:choice_menu
argchoice:Gotoh algorithm:gotoh_pair_wise
argchoice:Myers and Miller (slow):myers_miller_pair_wise
argchoice:FASTA (fast):fasta_pair_wise
argchoice:FASTA, check additional diagonals to convergence:cfasta_pair_wise
argvalue:3

arg:NDIAG
argtype:slider
arglabel:number of diagonals used by fasta_pair_wise
argmin:0
argmax:10
argvalue:0

arg:DIAGMODE
argtype:chooser
arglabel:score of diagonal is
argchoice:sum of exact matches:0
argchoice:best uninterrupted segment:1
argvalue:0

arg:NORMALIZE
argtype:slider
arglabel:Normalize score to
argmin:0
argmax:1000
argvalue:1000

arg:EXTEND
argtype:slider
arglabel:0 no extension; 1 extend all pairs; >1 extension threshold
argmin:0
argmax:100
argvalue:1

arg:GAPOPEN
argtype:slider
arglabel:Gap open penalty
argmin:-100
argmax:0
argvalue:-10

arg:GAPEXT
argtype:slider
arglabel:Gap extension penalty
argmin:-10
argmax:0
argvalue:-1


arg:COSPEN
argtype:slider
arglabel:Extension penalty for unalignable regions
argmin:-10
argmax:0
argvalue:-10

arg:TGMODE
arglabel:Terminal gaps
argtype:choice_menu
argchoice:penalized with gapopen + gap extension:0
argchoice:penalized with gap extension:1
argchoice:no penalty:2
argvalue:2

arg:TREEMODE
arglabel:Compute dendrogram using
argtype:choice_menu
argchoice:fasta dp_mode using pam250mt (very fast):very_fast
argchoice:fasta dp_mode using extended library (fast):fast
argchoice:chosen dp_mode using extended library (slow):slow
argvalue:0

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
# readseq -C makes sure that output is in capitals
# cut -f1 -d strips off the sequence length information that readseq generates on the name line
argchoice:GDE:readseq -C -p -f=PEARSON in1.msf_aln |sed -e 's/^>/%/' |cut -f1 -d" " >in1.result; (browser.csh file://$PWD/in1.score_html)& (gde in1.result; rm in1.result in1.score_html)&  ($GDE_TEXTEDIT in1.dnd;rm in1.dnd)&
argchoice:Output file:mv in1.msf_aln $OUTNAME.msf_aln; mv in1.dnd $OUTNAME.dnd; mv in1.score_html $OUTNAME.score_html; echo 'T_COFFEE completed'
argvalue:0

arg:OUTNAME
arglabel:Output file name
argtype:text

in:in1
informat:genbank
insave:


#------------------- mrtrans ( 7/ 7/04) ---------------------------------
item:mrtrans - protein/DNA alignment
# sed edits out ":CDS" or "_CDS" that is added by FEATURES
# tr gets rid of extra > and ASCII 128 added by mrtrans
# sed lops off the  comma and extra junk readseq adds to the name line
# mrtrans has been modified to allow sequence names longer than
# 9 char. Install mrtrans from mrtrans.tar.
# Finally, we have to translate the protein sequence to 
# uppercase, which is required by mrtrans.
itemmethod:(readseq -a -f=Pearson -C -pipe $PROTFILE |sed "s/[:_]CDS/_/" | sed "s/,.*//" >in1.prot; readseq -a -f=Pearson -pipe $DNAFILE |sed "s/[:_]CDS/_/" |sed "s/,.*//" | cut -f1 -d" " > in1.dna; mrtrans.csh in1.prot in1.dna; mrtrans in1.prot in1.dna.reordered | sed "s/> from >/>/" |tr -d '' | readseq -pipe -a -f2 | tr  -d '>'  > in1.gen; (gde in1.gen; $RM_CMD in1.gen)& $RM_CMD in1.prot in1.dna in1.dna.reordered)&

itemhelp:doc/fasta/mrtrans.txt
itemopen:gde_help_viewer.csh

arg:PROTFILE
argtype:text
arglabel:MULTIPLY-ALIGNED PROTEIN FILE
argtext:
 
arg:DNAFILE
argtype:text
arglabel:UNALIGNED DNA FILE
argtext:

# even though we don't use the in1 file, we still
# need to declare it to generate the unique name in1
in:in1
informat:genbank
insave:

#---------------------------- Sequence consensus ------------------------
item:Sequence Consensus
itemmethod:(MakeCons in1 $METHOD $MASK > out1)
itemhelp:doc/GDE/MakeCons.help
itemopen:gde_help_viewer.csh

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

#------------------------ Variable Positions -------------------------
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


#--------------- REFORM - print multiple alignment (2/11/05) -----------------
item:REFORM - print mult. align.
#Note: do not use flat or gde .
itemmethod:(tr '~' '-' < in1 |readseq -pipe -a -f8 | reform $TYPE -fp $GAPS $CAPS $DOTS -l$LINESIZE -s$START > in1.out; $GDE_TEXTEDIT in1.out;rm in1*) &
itemhelp: doc/xylem/reform.txt
itemopen:gde_help_viewer.csh

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:

#-------------------- Jalview 1.7b (BF 11/23/98) --------------------------
#

item:Jalview - protein alignment viewer
itemmethod:(tr "~" "-" <in1 | readseq -a -p -f=PEARSON | sed "s/:.*//" |sed "s/\*//" > in1.wrp; Jalview in1.wrp FASTA; rm in1 in1.wrp)&
itemhelp:
itemopen:gde_help_viewer.csh

in:in1
informat:genbank
insave:

#------ boxshade -  (12/23/98) Multiple Alignment formatter ---------
item:boxshade 3.2 - mult. align. -> graphics file
#Note: do not use flat or gde .
#The following files must be present in $DAT/boxshade:
#   box_dna.par   DNA parameter file 
#   box_pep.par   protein parameter file

itemmethod: (tr '~' '-' < in1 |readseq -pipe -a -form=MSF >in1.msf; rm in1; cp $DAT/boxshade/box_$PARAMTYPE.par in1.tmp; $PREEDIT boxshade -in=in1.msf -def -dev=1 -par=in1.par -sim=$DAT/boxshade/box_pep.sim -out=in1.ps; ($GDE_PSVIEW in1.ps; rm in1.ps)& rm in1.par) &
itemhelp: $DOC/boxshade/boxshade.asc
itemopen:gde_help_viewer.csh

arg:PARAMTYPE
argtype:chooser
argchoice:DNA:dna
argchoice:protein:pep
argvalue:1

arg:PREEDIT
argtype:chooser
arglabel:Preedit boxshade command file?
argchoice:Command file:mv in1.tmp in1.par; $GDE_TEXTEDIT in1.par;
argchoice:Empty file:echo "" >in1.par; rm in1.tmp; $GDE_TEXTEDIT in1.par;
argchoice:None:mv in1.tmp in1.par;
argvalue:0

in:in1
informat:genbank
insave:

#-------------------- Jalview 1.8 (BF  4/10/06) --------------------------
#

item:Jalview 1.8 (test) - protein alignment viewer
itemmethod:(tr "~" "-" <in1 | readseq -a -p -f=PEARSON | sed "s/:.*//" |sed "s/\*//" > in1.wrp; Jalview-1.8 in1.wrp FASTA; rm in1 in1.wrp)&
itemhelp:doc/jalview/help.html
itemopen:gde_help_viewer.csh

in:in1
informat:genbank
insave:


############################## Primers ##############################
menu:Primers

#--------------------- PRIMER 3  (4/10/06) -----------------------
item:PRIMER 3
itemlabel:PRIMER 3 (Whitehead Institute)
itemmethod: (primer3.csh in1 $MAXPRIMERS $OPTLEN $MINLEN $MAXLEN $OPTTEMP $MINTEMP $MAXTEMP $MINGC $MAXGC $SALTCONC $DNACONC $MAXUNK $MAXSELF $MAX3PSELF $GCCLAMP $MINPROD $MAXPROD $intoligo $ioptlen $iminlen $imaxlen $iopttemp $imintemp $imaxtemp $imingc $imaxgc $isaltconc $idnaconc $imaxunk $imaxself $imax3pself > in1.in; primer3run.csh in1.in)& 
itemhelp:doc/primer/primer3.html
itemopen:gde_help_viewer.csh

arg:MAXPRIMERS
argtype:slider
arglabel: Find the N best primer pairs/internal oligos (N):
argmin:1
argmax:30
argvalue:5

arg:OPTLEN
argtype:slider
arglabel:optimal    PRIMER LENGTH
argmin:10
argmax:50
argvalue:20

arg:MINLEN
argtype:slider
arglabel:minimum    PRIMER LENGTH
argmin:10
argmax:50
argvalue:18

arg:MAXLEN
argtype:slider
arglabel:maximum    PRIMER LENGTH
argmin:10
argmax:50
argvalue:22

arg:OPTTEMP
argtype:slider
arglabel:optimal    PRIMER Tm
argmin:30
argmax:100
argvalue:60

arg:MINTEMP
argtype:slider
arglabel:minimum    PRIMER Tm
argmin:30
argmax:100
argvalue:57

arg:MAXTEMP
argtype:slider
arglabel:maximum    PRIMER Tm
argmin:30
argmax:100
argvalue:63

arg:MINGC
argtype:slider
arglabel:minimum    %GC
argmin:20
argmax:80
argvalue:20

arg:MAXGC
argtype:slider
arglabel:maximum    %GC
argmin:20
argmax:80
argvalue:80

arg:SALTCONC
argtype:slider
arglabel:SALT concentration (mM)
argmin:10
argmax:500
argvalue:50

arg:DNACONC
argtype:slider
arglabel:DNA   concentration (nM)
argmin:1
argmax:100
argvalue:50

arg:MAXUNK
argtype:slider
arglabel:maximum UNKNOWN BASES (Ns) allowed in primer
argmin:0
argmax:5
argvalue:0

arg:MAXSELF
argtype:slider
arglabel:maximum primer SELF-COMPLEMENTARITY
argmin:0
argmax:20
argvalue:12

arg:MAX3PSELF
argtype:slider
arglabel:maximum primer 3' END SELF-COMPLEMENTARITY
argmin:0
argmax:20
argvalue:8

arg:GCCLAMP
argtype:slider
arglabel:GC CLAMP (how many 3' bases?)
argmin:0
argmax:5
argvalue:0

arg:MINPROD
argtype:slider
arglabel:minimum PRODUCT LENGTH
argmin:100
argmax:3000
argvalue:100

arg:MAXPROD
argtype:slider
arglabel:maximum PRODUCT LENGTH
argmin:100
argmax:3000
argvalue:500

arg:intoligo
argtype:chooser
arglabel:===========FIND AN OLIGO INTERNAL TO PCR FRAGMENT?========
argchoice:Yes:1
argchoice:No:0
argvalue:1

arg:ioptlen
argtype:slider
arglabel:optimal    OLIGO LENGTH
argmin:10
argmax:50
argvalue:20

arg:iminlen
argtype:slider
arglabel:minimum    OLIGO LENGTH
argmin:10
argmax:50
argvalue:18

arg:imaxlen
argtype:slider
arglabel:maximum    OLIGO LENGTH
argmin:10
argmax:50
argvalue:27

arg:iopttemp
argtype:slider
arglabel:optimal    OLIGO Tm
argmin:30
argmax:100
argvalue:60

arg:imintemp
argtype:slider
arglabel:minimum    OLIGO Tm
argmin:30
argmax:100
argvalue:57

arg:imaxtemp
argtype:slider
arglabel:maximum    OLIGO Tm
argmin:30
argmax:100
argvalue:63

arg:imingc
argtype:slider
arglabel:minimum    %GC
argmin:20
argmax:80
argvalue:20

arg:imaxgc
argtype:slider
arglabel:maximum    %GC
argmin:20
argmax:80
argvalue:80

arg:isaltconc
argtype:slider
arglabel:SALT concentration (mM)
argmin:10
argmax:500
argvalue:50

arg:idnaconc
argtype:slider
arglabel:DNA   concentration (nM)
argmin:1
argmax:100
argvalue:50

arg:imaxunk
argtype:slider
arglabel:maximum UNKNOWN BASES (Ns) allowed in OLIGO
argmin:0
argmax:5
argvalue:0

arg:imaxself
argtype:slider
arglabel:maximum OLIGO SELF-COMPLEMENTARITY
argmin:0
argmax:20
argvalue:12

arg:imax3pself
argtype:slider
arglabel:maximum OLIGO 3' END SELF-COMPLEMENTARITY
argmin:0
argmax:20
argvalue:12

in:in1
informat:flat
insave:

#----------------------- MWCalculator 1.0 (8/9/98)  ---------------------
item:MWCalculator
itemlabel:Calculate Mol. Wts.
itemmethod: (MWCalculator )&


############################## Phylogeny ##############################
menu:Phylogeny

#------------------------- Phylip documentation (12/20/04) --------------------------
item:Phylip documentation
itemmethod:($BIRCH_NETSCAPE $DOC/Phylip/main.html)&




#------------------------- Phylip ( 4/10/2006)  --------------------------
item:Phylip
# sed edits out ":CDS" that is added by FEATURES
itemmethod:mkdir in1.dir; sed "s/[:].*//" in1 | readseq -a -f12 -pipe | sed "s/ YF//1" > in1.dir/infile; rm in1; cd in1.dir; (nice -n 10 $GDE_TERM $PROGRAM; $WHERE) &
itemhelp:doc/Phylip/main.html
itemopen:gde_help_viewer.csh
 
arg:PROGRAM
argtype:choice_menu
arglabel:WHICH PROGRAM TO RUN?
argchoice:DNAPARS:dnapars
argchoice:DNAPENNY:dnapenny
argchoice:DNAML:dnaml
argchoice:DNAMLK:dnamlk
argchoice:DNACOMP:dnacomp
argchoice:DNAMOVE:dnamove
argchoice:DNAINVAR:dnainvar
argchoice:PROTPARS:protpars
argchoice:PROML:proml  
argchoice:PROMLK:promlk 


arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:ATV:mv outfile ../in1.outfile; mv outtree ../in1.treefile; cd ..; rm -r in1.dir; ($GDE_TEXTEDIT in1.outfile; rm in1.outfile) & ($GDE_TEXTEDIT in1.treefile; rm in1.treefile) & (atv in1.treefile; rm in1.treefile) &
argchoice:Drawtree:mv outfile ../in1.outfile; (cd ..; $GDE_TEXTEDIT in1.outfile; rm in1.outfile)& (cp outtree ../in1.treefile; cd ..; $GDE_TEXTEDIT in1.treefile; rm in1.treefile) & (mv outtree intree; cp $DAT/Phylip/font1 fontfile; drawtree.csh l yes f 0 360 IE 360 reg 0.333 | nice -n 10 drawtree; $GDE_PSVIEW plotfile; cd ..; rm -r in1.dir) &
argchoice:Output files:mv outfile ../$OUTNAME.outfile; mv outtree ../$OUTNAME.treefile; cd ..; rm -r in1.dir
argvalue:0
 
arg:OUTNAME
arglabel:raw name
argtype:text

in:in1
informat:genbank

#-------------------- DNA distance methods  ( 6/ 3/2006) ------------------
item:DNA Distance methods
# sed edits out ":CDS" that is added by FEATURES
itemmethod:tr "~" "-" < in1 | sed "s/[\:\_]CDS/_/" | readseq -a -f12 -pipe | sed "s/ YF//1" > in1.tmp; rm in1; (dnadist.csh in1.tmp $DMETHOD $TRANSRATIO $METHOD $BSEED $REPLICATES $BLOCKSIZE $PERCENT $TCONMETH $POWER $SUBREP $GLOBAL $NEGBRANCH $OUTGRP $JUMBLE $JSEED $NUMJUM $TERMOUT $PRINTDATA in1.outfile in1.outtree; rm in1.tmp; $WHERE) &
itemhelp:doc/Phylip/dnadist.html
itemopen:gde_help_viewer.csh
 
arg:DMETHOD
argtype:choice_menu
arglabel:DISTANCE MATRIX METHOD
argchoice:F84:f
argchoice:Kimura 2-parameter:k
argchoice:Jukes-Cantor:j
argchoice:Log of the determinant:l
argvalue:0  

arg:TRANSRATIO
arglabel:TRANSITION/TRANSVERSION RATIO
argtype:slider
argmin:1
argmax:20
argvalue:2

arg:METHOD
argtype:choice_menu
arglabel:RESAMPLING (SLOW!)
argchoice:none:n
argchoice:Bootstrap:b
argchoice:Delete-half jackinfe:d
argchoice:Permute species for each character:ps
argchoice:Permute character order:po
argchoice:Permute within species:pw
argvalue:0   

arg:BSEED
argtype:slider
arglabel:_____Bootstrap random number seed
argmin:5
argmax:65535
argvalue:12345

arg:REPLICATES
argtype:slider
arglabel:_____Number of bootstrap replicates?
argmin:1
argmax:1000
argvalue:100

arg:BLOCKSIZE
argtype:slider
arglabel:_____Block size (Bootstrap only)
argmin:1
argmax:50
argvalue:1

arg:PERCENT
argtype:slider
arglabel:_____Percent of sites to sample
argmin:1
argmax:100
argvalue:100

arg:TCONMETH
arglabel:TREE CONSTRUCTION METHOD
argtype:choice_menu
argchoice:Weighbor, weighted Neighbor Joining:w
argchoice:FITCH, Fitch-Margoliash:F
argchoice:FITCH, Minimum Evolution:f
argchoice:KITSCH, Fitch-Margoliash constant evolutionary clock:K
argchoice:KITSCH, Minimum Evolution constant evolutionary clock:k
argchoice:Neighbor Joining:N
argchoice:UPGMA:U
argvalue:0

arg:POWER
arglabel:POWER (FITCH,KITCH only)
argtype:text
argtext:2.0

arg:NEGBRANCH
arglabel:ALLOW NEGATIVE BRANCH LENGTHS? (FITCH,KITCH only)
argtype:chooser
argchoice:Yes:y
argchoice:No:n
argvalue:1

arg:OUTGRP
arglabel:SEQUENCE # OF OUTGROUP:
argtype:slider
argmin:1
argmax:1000
argvalue:1

arg:SUBREP
arglabel:DO SUBREPLICATES?
argtype:chooser
argchoice:Yes:y
argchoice:No:n
argvalue:0

arg:GLOBAL
arglabel:DO GLOBAL REARRANGEMENTS?  (FITCH,KITCH only)
argtype:chooser
argchoice:Yes:y
argchoice:No:n
argvalue:0

arg:JUMBLE
argtype:chooser
arglabel:JUMBLE THE SEQUENCE ORDER?
argchoice:Yes:J
argchoice:No:n
argvalue:0   

arg:JSEED
argtype:slider
arglabel:_____Jumble random number seed
argmin:5
argmax:65535
argvalue:12345

arg:NUMJUM
argtype:slider
arglabel:_____Number of times to jumble
argmin:1
argmax:50
argvalue:1

arg:TERMOUT
argtype:chooser
arglabel:SHOW PROGRESS REPORT
argchoice:none:/dev/null
argchoice:on screen:/dev/tty
argchoice:to .log file:../../$OUTNAME.log
argvalue:0

arg:PRINTDATA
argtype:chooser
arglabel:PRINT SEQUENCE DATA TO OUTFILE?
argchoice:Yes:y
argchoice:No:n
argvalue:1   

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Tree editor:gde.treeoutput.csh -e in1.outtree in1.outfile $OUTNAME
argchoice:Drawing program:gde.treeoutput.csh -d in1.outtree in1.outfile $OUTNAME
argchoice:Output files:gde.treeoutput.csh -f in1.outtree in1.outfile $OUTNAME
argvalue:0

#arg:WHERE
#arglabel:WHERE TO SEND OUTPUT
#argtype:chooser
#argchoice:ATV: ($GDE_TEXTEDIT in1.outfile; rm in1.outfile)& (atv in1.outtree)& ($GDE_TEXTEDIT in1.outtree; rm in1.outtree)&  
#argchoice:Drawtree:($GDE_TEXTEDIT in1.outfile; rm in1.outfile)&  (drawtree.csh in1.outtree yes f 0 360 IE 360 reg $DAT/Phylip/font1 0.333 l in1.plotfile; $GDE_PSVIEW in1.plotfile; rm in1.plotfile)& ($GDE_TEXTEDIT in1.outtree; rm in1.outtree) &
#argchoice:Output files:mv in1.outfile $OUTNAME.outfile; mv in1.outtree $OUTNAME.treefile
#argvalue:0
 
arg:OUTNAME
arglabel:_____raw filename (no extension)
argtype:text
argtext:dnadist

in:in1
informat:genbank

#-------------------- Protein distance methods  ( 6/ 3/2006) ------------------
item:Protein Distance methods
# sed edits out ":CDS" that is added by FEATURES
itemmethod:tr "~" "-" < in1 | sed "s/[\:\_]CDS/_/" | readseq -a -f12 -pipe | sed "s/ YF//1" > in1.tmp; rm in1; (protdist.csh in1.tmp $DMETHOD $TRANSRATIO $GC $CATEGORIZATION $METHOD $BSEED $REPLICATES $BLOCKSIZE $PERCENT $TCONMETH $POWER $SUBREP $GLOBAL $NEGBRANCH $OUTGRP $JUMBLE $JSEED $NUMJUM $TERMOUT $PRINTDATA in1.outfile in1.outtree; rm in1.tmp; $WHERE) &
itemhelp:doc/Phylip/protdist.html
itemopen:gde_help_viewer.csh
 
arg:DMETHOD
argtype:choice_menu
arglabel:DISTANCE MATRIX METHOD
argchoice:Jones-Taylor-Thornton:J
argchoice:Henikoff-Tiller PMB:H
argchoice:Dayhoff PAM:D
argchoice:Kimura:K
argchoice:Categories:C
argvalue:0  

arg:TRANSRATIO
arglabel:_____Transition/Transversion ratio (Categories only)
argtype:slider
argmin:1
argmax:20
argvalue:2

arg:GC
argtype:choice_menu
arglabel:_____Genetic Code (Categories only)
argchoice:Universal:u
argchoice:Mitochondrial:m
argchoice:Vertebrate mitochondrial:v
argchoice:Fly mitochondrial:f
argchoice:Yeast mitochondrial:y
argvalue:0

arg:CATEGORIZATION
argtype:choice_menu
arglabel:_____Categories of amino acids (Categories only)
argchoice:George-Hunt-Barker:G
argchoice:Chemical:C
argchoice:Hall:H
argvalue:0  
   
arg:METHOD
argtype:choice_menu
arglabel:RESAMPLING (SLOW!)
argchoice:none:n
argchoice:Bootstrap:b
argchoice:Delete-half jackinfe:d
argchoice:Permute species for each character:ps
argchoice:Permute character order:po
argchoice:Permute within species:pw
argvalue:0   

arg:BSEED
argtype:slider
arglabel:_____Bootstrap random number seed
argmin:5
argmax:65535
argvalue:12345

arg:REPLICATES
argtype:slider
arglabel:_____Number of bootstrap replicates?
argmin:1
argmax:1000
argvalue:100

arg:BLOCKSIZE
argtype:slider
arglabel:_____Block size (Bootstrap only)
argmin:1
argmax:50
argvalue:1

arg:PERCENT
argtype:slider
arglabel:_____Percent of sites to sample
argmin:1
argmax:100
argvalue:100

arg:TCONMETH
arglabel:TREE CONSTRUCTION METHOD
argtype:choice_menu
argchoice:Weighbor, weighted Neighbor Joining:w
argchoice:FITCH, Fitch-Margoliash:F
argchoice:FITCH, Minimum Evolution:f
argchoice:KITSCH, Fitch-Margoliash constant evolutionary clock:K
argchoice:KITSCH, Minimum Evolution constant evolutionary clock:k
argchoice:Neighbor Joining:N
argchoice:UPGMA:U
argvalue:0

arg:POWER
arglabel:POWER (FITCH,KITCH only)
argtype:text
argtext:2.0

arg:NEGBRANCH
arglabel:ALLOW NEGATIVE BRANCH LENGTHS? (FITCH,KITCH only)
argtype:chooser
argchoice:Yes:y
argchoice:No:n
argvalue:1

arg:OUTGRP
arglabel:SEQUENCE # OF OUTGROUP:
argtype:slider
argmin:1
argmax:1000
argvalue:1

arg:SUBREP
arglabel:DO SUBREPLICATES?
argtype:chooser
argchoice:Yes:y
argchoice:No:n
argvalue:0

arg:GLOBAL
arglabel:DO GLOBAL REARRANGEMENTS?  (FITCH,KITCH only)
argtype:chooser
argchoice:Yes:y
argchoice:No:n
argvalue:0

arg:JUMBLE
argtype:chooser
arglabel:JUMBLE THE SEQUENCE ORDER?
argchoice:Yes:J
argchoice:No:n
argvalue:0   

arg:JSEED
argtype:slider
arglabel:_____Jumble random number seed
argmin:5
argmax:65535
argvalue:12345

arg:NUMJUM
argtype:slider
arglabel:_____Number of times to jumble
argmin:1
argmax:50
argvalue:1

arg:TERMOUT
argtype:chooser
arglabel:SHOW PROGRESS REPORT
argchoice:none:/dev/null
argchoice:on screen:/dev/tty
argchoice:to .log file:../../$OUTNAME.log
argvalue:0

arg:PRINTDATA
argtype:chooser
arglabel:PRINT SEQUENCE DATA TO OUTFILE?
argchoice:Yes:y
argchoice:No:n
argvalue:1   

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Tree editor:gde.treeoutput.csh -e in1.outtree in1.outfile $OUTNAME
argchoice:Drawing program:gde.treeoutput.csh -d in1.outtree in1.outfile $OUTNAME
argchoice:Output files:gde.treeoutput.csh -f in1.outtree in1.outfile $OUTNAME
argvalue:0

#arg:WHERE
#arglabel:WHERE TO SEND OUTPUT
#argtype:chooser
#argchoice:ATV: ($GDE_TEXTEDIT in1.outfile; rm in1.outfile)& (atv in1.outtree)& ($GDE_TEXTEDIT in1.outtree; rm in1.outtree)&  
#argchoice:Drawtree:($GDE_TEXTEDIT in1.outfile; rm in1.outfile)&  (drawtree.csh in1.outtree yes f 0 360 IE 360 reg $DAT/Phylip/font1 0.333 l in1.plotfile; $GDE_PSVIEW in1.plotfile; rm in1.plotfile)& ($GDE_TEXTEDIT in1.outtree; rm in1.outtree) &
#argchoice:Output files:mv in1.outfile $OUTNAME.outfile; mv in1.outtree $OUTNAME.treefile
#argvalue:0
 
arg:OUTNAME
arglabel:_____raw filename (no extension)
argtype:text
argtext:protdist

in:in1
informat:genbank

#------------------------- DNAPARS ( 4/10/2006)  --------------------------
item:DNAPARS - Parsimony
# sed edits out ":CDS" that is added by FEATURES
itemmethod:tr "~" "-" < in1 | sed "s/[\:\_]CDS/_/" | readseq -a -f12 -pipe | sed "s/ YF//1" > in1.infile; rm in1; (dnapars.csh in1.infile $SOPTION $METHOD $BSEED $REPLICATES $PERCENT $BLOCKSIZE $JUMBLE $JSEED $NUMJUM $OUTGROUP $PARSTYPE $THRESHOLD $TRANSVERSION $TERMOUT $PRINTDATA in1.outfile in1.outtree; $RM_CMD in1.infile; $WHERE) &
itemhelp:doc/Phylip/dnapars.html
itemopen:gde_help_viewer.csh

arg:SOPTION
argtype:chooser
arglabel:TREE REARRANGEMENT
argchoice:More thorough (default):m
argchoice:Less thorough:l
argchoice:Rearrange on just one best tree:r
argvalue:0   

arg:OUTGROUP
argtype:slider
arglabel:SEQUENCE TO USE FOR OUTGROUP
argmin:1
argmax:1000
argvalue:1

arg:PARSTYPE
argtype:chooser
arglabel:
argchoice:Regular parsimony:p
argchoice:Threshold parsimony:t
argvalue:0   

arg:THRESHOLD
argtype:slider
arglabel:_____threshold
argmin:2
argmax:10
argvalue:2

arg:TRANSVERSION
argtype:chooser
argchoice:Count all steps:a
argchoice:Count only transversions:t
argvalue:0
 
arg:METHOD
argtype:choice_menu
arglabel:RESAMPLING (SLOW!)
argchoice:none:n
argchoice:Bootstrap:b
argchoice:Delete-half jackinfe:d
argchoice:Permute species for each character:ps
argchoice:Permute character order:po
argchoice:Permute within species:pw
argvalue:0   

arg:BSEED
argtype:slider
arglabel:_____Bootstrap random number seed
argmin:5
argmax:65535
argvalue:12345

arg:REPLICATES
argtype:slider
arglabel:_____Number of bootstrap replicates?
argmin:1
argmax:1000
argvalue:100

arg:BLOCKSIZE
argtype:slider
arglabel:_____Block size (Bootstrap only)
argmin:1
argmax:50
argvalue:1

arg:PERCENT
argtype:slider
arglabel:_____Percent of sites to sample
argmin:1
argmax:100
argvalue:100


arg:JUMBLE
argtype:chooser
arglabel:JUMBLE THE SEQUENCE ORDER?
argchoice:Yes:J
argchoice:No:n
argvalue:0   

arg:JSEED
argtype:slider
arglabel:_____Jumble random number seed
argmin:5
argmax:65535
argvalue:12345

arg:NUMJUM
argtype:slider
arglabel:_____Number of times to jumble
argmin:1
argmax:50
argvalue:1

arg:TERMOUT
argtype:chooser
arglabel:SHOW PROGRESS REPORT
argchoice:none:/dev/null
argchoice:on screen:/dev/tty
argchoice:to .log file:../../$OUTNAME.log
argvalue:0

arg:PRINTDATA
argtype:chooser
arglabel:PRINT SEQUENCE DATA TO OUTFILE?
argchoice:Yes:y
argchoice:No:n
argvalue:1   

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Tree editor:gde.treeoutput.csh -e in1.outtree in1.outfile $OUTNAME
argchoice:Drawing program:gde.treeoutput.csh -d in1.outtree in1.outfile $OUTNAME
argchoice:Output files:gde.treeoutput.csh -f in1.outtree in1.outfile $OUTNAME
argvalue:0
  
arg:OUTNAME
arglabel:_____raw filename (no extension)
argtype:text
argtext:dnapars

in:in1
informat:genbank
insave:

#------------------------- PROTPARS ( 4/10/2006)  --------------------------
item:PROTPARS - Protein Parsimony
# sed edits out ":CDS" that is added by FEATURES
itemmethod:tr "~" "-" < in1 | sed "s/[\:\_]CDS/_/" | readseq -a -f12 -pipe | sed "s/ YF//1" > in1.infile; rm in1; (protpars.csh in1.infile $METHOD $BSEED $REPLICATES $PERCENT $BLOCKSIZE $JUMBLE $JSEED $NUMJUM $OUTGROUP $PARSTYPE $THRESHOLD $GC $TERMOUT $PRINTDATA in1.outfile in1.outtree; $RM_CMD in1.infile; $WHERE)&
itemhelp:doc/Phylip/protpars.html
itemopen:gde_help_viewer.csh


arg:OUTGROUP
argtype:slider
arglabel:SEQUENCE TO USE FOR OUTGROUP
argmin:1
argmax:1000
argvalue:1

arg:PARSTYPE
arglabel:
argtype:chooser
argchoice:Regular parsimony:p
argchoice:Threshold parsimony:t
argvalue:0   

arg:THRESHOLD
argtype:slider
arglabel:_____threshold
argmin:2
argmax:10
argvalue:2

arg:GC
argtype:choice_menu
arglabel:GENETIC CODE
argchoice:Universal:u
argchoice:Mitochondrial:m
argchoice:Vertebrate mitochondrial:v
argchoice:Fly mitochondrial:f
argchoice:Yeast mitochondrial:y
argvalue:0   
 
arg:METHOD
argtype:choice_menu
arglabel:RESAMPLING (SLOW!)
argchoice:none:n
argchoice:Bootstrap:b
argchoice:Delete-half jackinfe:d
argchoice:Permute species for each character:ps
argchoice:Permute character order:po
argchoice:Permute within species:pw
argvalue:0   

arg:BSEED
argtype:slider
arglabel:_____Bootstrap random number seed
argmin:5
argmax:65535
argvalue:12345

arg:REPLICATES
argtype:slider
arglabel:_____Number of bootstrap replicates?
argmin:1
argmax:1000
argvalue:100

arg:BLOCKSIZE
argtype:slider
arglabel:_____Block size (Bootstrap only)
argmin:1
argmax:50
argvalue:1

arg:PERCENT
argtype:slider
arglabel:_____Percent of sites to sample
argmin:1
argmax:100
argvalue:100


arg:JUMBLE
argtype:chooser
arglabel:JUMBLE THE SEQUENCE ORDER?
argchoice:Yes:J
argchoice:No:n
argvalue:0   

arg:JSEED
argtype:slider
arglabel:_____Jumble random number seed
argmin:5
argmax:65535
argvalue:12345

arg:NUMJUM
argtype:slider
arglabel:_____Number of times to jumble
argmin:1
argmax:50
argvalue:1

arg:TERMOUT
argtype:chooser
arglabel:SHOW PROGRESS REPORT
argchoice:none:/dev/null
argchoice:on screen:/dev/tty
argchoice:to .log file:../../$OUTNAME.log
argvalue:0

arg:PRINTDATA
argtype:chooser
arglabel:PRINT SEQUENCE DATA TO OUTFILE?
argchoice:Yes:y
argchoice:No:n
argvalue:1   

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Tree editor:gde.treeoutput.csh -e in1.outtree in1.outfile $OUTNAME
argchoice:Drawing program:gde.treeoutput.csh -d in1.outtree in1.outfile $OUTNAME
argchoice:Output files:gde.treeoutput.csh -f in1.outtree in1.outfile $OUTNAME
argvalue:0
  
arg:OUTNAME
arglabel:_____raw filename (no extension)
argtype:text
argtext:protpars

in:in1
informat:genbank
insave:



#------------------------- DNAML ( 9/ 5/2007)  --------------------------
item:DNAML - DNA Maximum Likelihood
# sed edits out ":CDS" that is added by FEATURES
itemmethod:tr "~" "-" < in1 | sed "s/[\:\_]CDS/_/" | readseq -a -f12 -pipe | sed "s/ YF//1" > in1.tmp; rm in1; (dnaml.csh in1.tmp $UTREE $UFN $PROGRAM $TRATIO $SPEEDY $GLOBAL $METHOD $BSEED $REPLICATES $BLOCKSIZE $PERCENT $JUMBLE $JSEED $NUMJUM $OUTGRP $TERMOUT $PRINTDATA in1.outfile in1.outtree; rm in1.tmp; $WHERE) &
itemhelp:doc/Phylip/dnaml.html
itemopen:gde_help_viewer.csh

arg:UTREE
argtype:chooser
argchoice:Search for best tree:n
argchoice:Evaluate user-supplied tree:y
argvalue:0

arg:UFN
arglabel:_____User tree filename:
argtype:text
argtext:none

arg:PROGRAM
argtype:chooser
argchoice:DNAML:dnaml
argchoice:DNAMLK (constant molecular clock):dnamlk
argvalue:0

arg:TRATIO
arglabel:TRANSITION/TRANSVERSION RATIO
argtype:slider
argmin:1
argmax:20
argvalue:2

arg:SPEEDY
arglabel:SPEEDIER BUT ROUGHER ANALYSIS?
argtype:chooser
argchoice:Yes:y
argchoice:No:n
argvalue:0

arg:GLOBAL
arglabel:DO GLOBAL REARRANGEMENTS?
argtype:chooser
argchoice:Yes:y
argchoice:No:n
argvalue:0

arg:OUTGRP
arglabel:SEQUENCE # OF OUTGROUP:
argtype:slider
argmin:1
argmax:1000
argvalue:1

arg:METHOD
argtype:choice_menu
arglabel:RESAMPLING (SLOW!)
argchoice:none:n
argchoice:Bootstrap:b
argchoice:Delete-half jackinfe:d
argchoice:Permute species for each character:ps
argchoice:Permute character order:po
argchoice:Permute within species:pw
argvalue:0   

arg:BSEED
argtype:slider
arglabel:_____Bootstrap random number seed
argmin:5
argmax:65535
argvalue:12345

arg:REPLICATES
argtype:slider
arglabel:_____Number of bootstrap replicates?
argmin:1
argmax:1000
argvalue:100

arg:BLOCKSIZE
argtype:slider
arglabel:_____Block size (Bootstrap only)
argmin:1
argmax:50
argvalue:1

arg:PERCENT
argtype:slider
arglabel:_____Percent of sites to sample
argmin:1
argmax:100
argvalue:100

arg:JUMBLE
argtype:chooser
arglabel:JUMBLE THE SEQUENCE ORDER?
argchoice:Yes:J
argchoice:No:n
argvalue:0   

arg:JSEED
argtype:slider
arglabel:_____Jumble random number seed
argmin:5
argmax:65535
argvalue:12345

arg:NUMJUM
argtype:slider
arglabel:_____Number of times to jumble
argmin:1
argmax:50
argvalue:1

arg:TERMOUT
argtype:chooser
arglabel:SHOW PROGRESS REPORT
argchoice:none:/dev/null
argchoice:on screen:/dev/tty
argchoice:to .log file:../../$OUTNAME.log
argvalue:0

arg:PRINTDATA
argtype:chooser
arglabel:PRINT SEQUENCE DATA TO OUTFILE?
argchoice:Yes:y
argchoice:No:n
argvalue:1   

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Tree editor:gde.treeoutput.csh -e in1.outtree in1.outfile $OUTNAME
argchoice:Drawing program:gde.treeoutput.csh -d in1.outtree in1.outfile $OUTNAME
argchoice:Output files:gde.treeoutput.csh -f in1.outtree in1.outfile $OUTNAME
argvalue:0
 
arg:OUTNAME
arglabel:_____raw filename (no extension)
argtype:text
argtext:dnaml

in:in1
informat:genbank
insave:


#------------------------- PROML ( 4/10/2006)  --------------------------
item:PROML - Protein Maximum Likelihood
# sed edits out ":CDS" that is added by FEATURES
itemmethod:tr "~" "-" < in1 | sed "s/[\:\_]CDS/_/" | readseq -a -f12 -pipe | sed "s/ YF//1" > in1.tmp; rm in1; (proml.csh in1.tmp $UTREE $UFN $PROGRAM $PMODEL $SPEEDY $GLOBAL $METHOD $BSEED $REPLICATES $BLOCKSIZE $PERCENT $JUMBLE $JSEED $NUMJUM $OUTGRP $TERMOUT $PRINTDATA in1.outfile in1.outtree; rm in1.tmp; $WHERE) &
itemhelp:doc/Phylip/proml.html
itemopen:gde_help_viewer.csh

arg:UTREE
argtype:chooser
argchoice:Search for best tree:n
argchoice:Evaluate user-supplied tree:y
argvalue:0

arg:UFN
arglabel:_____User tree filename:
argtype:text
argtext:none

arg:PROGRAM
argtype:chooser
argchoice:PROML:proml
argchoice:PROMLK (assumes constant molecular clock):promlk
argvalue:0

arg:PMODEL
argtype:choice_menu
arglabel:PROBABILITY MODEL
argchoice:Jones-Taylor-Thornton:j
argchoice:Henikoff/Tiller PMB:h
argchoice:Dayhoff PAM:d
argvalue:0   

arg:SPEEDY
arglabel:SPEEDIER BUT ROUGHER ANALYSIS?
argtype:chooser
argchoice:Yes:y
argchoice:No:n
argvalue:0

arg:GLOBAL
arglabel:DO GLOBAL REARRANGEMENTS?
argtype:chooser
argchoice:Yes:y
argchoice:No:n
argvalue:0


arg:OUTGRP
arglabel:SEQUENCE # OF OUTGROUP:
argtype:slider
argmin:1
argmax:1000
argvalue:1

arg:METHOD
argtype:choice_menu
arglabel:RESAMPLING (SLOW!)
argchoice:none:n
argchoice:Bootstrap:b
argchoice:Delete-half jackinfe:d
argchoice:Permute species for each character:ps
argchoice:Permute character order:po
argchoice:Permute within species:pw
argvalue:0   

arg:BSEED
argtype:slider
arglabel:_____Bootstrap random number seed
argmin:5
argmax:65535
argvalue:12345

arg:REPLICATES
argtype:slider
arglabel:_____Number of bootstrap replicates?
argmin:1
argmax:1000
argvalue:100

arg:BLOCKSIZE
argtype:slider
arglabel:_____Block size (Bootstrap only)
argmin:1
argmax:50
argvalue:1

arg:PERCENT
argtype:slider
arglabel:_____Percent of sites to sample
argmin:1
argmax:100
argvalue:100

arg:JUMBLE
argtype:chooser
arglabel:JUMBLE THE SEQUENCE ORDER?
argchoice:Yes:J
argchoice:No:n
argvalue:0   

arg:JSEED
argtype:slider
arglabel:_____Jumble random number seed
argmin:5
argmax:65535
argvalue:12345

arg:NUMJUM
argtype:slider
arglabel:_____Number of times to jumble
argmin:1
argmax:50
argvalue:1

arg:TERMOUT
argtype:chooser
arglabel:SHOW PROGRESS REPORT
argchoice:none:/dev/null
argchoice:on screen:/dev/tty
argchoice:to .log file:../../$OUTNAME.log
argvalue:0

arg:PRINTDATA
argtype:chooser
arglabel:PRINT SEQUENCE DATA TO OUTFILE?
argchoice:Yes:y
argchoice:No:n
argvalue:1   

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Tree editor:gde.treeoutput.csh -e in1.outtree in1.outfile $OUTNAME
argchoice:Drawing program:gde.treeoutput.csh -d in1.outtree in1.outfile $OUTNAME
argchoice:Output files:gde.treeoutput.csh -f in1.outtree in1.outfile $OUTNAME
argvalue:0

#arg:WHERE
#arglabel:WHERE TO SEND OUTPUT
#argtype:chooser
#argchoice:ATV: ($GDE_TEXTEDIT in1.outfile; rm in1.outfile)& (atv in1.outtree)& ($GDE_TEXTEDIT in1.outtree; rm in1.outtree)&  
#argchoice:Drawtree:($GDE_TEXTEDIT in1.outfile; rm in1.outfile)&  (drawtree.csh in1.outtree yes f 0 360 IE 360 reg $DAT/Phylip/font1 0.333 l in1.plotfile; $GDE_PSVIEW in1.plotfile; rm in1.plotfile)& ($GDE_TEXTEDIT in1.outtree; rm in1.outtree) &
#argchoice:Output files:mv in1.outfile $OUTNAME.outfile; mv in1.outtree $OUTNAME.treefile
#argvalue:0
 
arg:OUTNAME
arglabel:_____raw filename (no extension)
argtype:text
argtext:dnaml

in:in1
informat:genbank
insave:

#------------------------- fastDNAml (2/17/2003)  --------------------------
item:fastDNAml
# sed edits out ":CDS" that is added by FEATURES
itemmethod:sed "s/[:].*//" in1 | readseq -a -f12 -pipe | sed "s/ YF//1" > in1.tmp; rm in1; (fastDNAml.csh in1.tmp $QADD $GLOBAL $JMBLE $JSEED $BSTRAP $TRATIO $SPOUT $OUTGRP $USERTREE $UFN > in1.infile; rm in1.tmp; $PREEDIT fastDNAmlrun.csh in1.infile $BSTRAP $BSEED $BNUM in1 $HOST; rm in1.infile; $WHERE) &
itemhelp:doc/Phylip/fastDNAml/fastDNAml_doc.txt
itemopen:gde_help_viewer.csh

arg:GLOBAL
arglabel:DO GLOBAL REARRANGEMENTS?
argtype:chooser
argchoice:Yes:Y
argchoice:No:N
argvalue:0

arg:QADD
arglabel:QUICKADD?
argtype:chooser
argchoice:Yes:Y
argchoice:No:N
argvalue:0

arg:TRATIO
arglabel:TRANSITION/TRANSVERSION RATIO
argtype:text
argtext:2.0

arg:BSTRAP
arglabel:BOOTSTRAP THE DATA?
argtype:chooser
argchoice:Yes:y
argchoice:No:N
argvalue:1

arg:BSEED
argtype:slider
arglabel:Bootstrap random number seed
argmin:0
argmax:65535
argvalue:12345

arg:BNUM
argtype:slider
arglabel:# of bootstrap replicates
argmin:0
argmax:1000
argvalue:50

arg:JMBLE
arglabel:JUMBLE (RANDOMIZE) SEQUENCE ADDITION ORDER?
argtype:chooser
argchoice:Yes:Y
argchoice:No:N
argvalue:1

arg:JSEED
argtype:slider
arglabel:Jumble random number seed
argmin:0
argmax:65535
argvalue:12345

arg:SPOUT
arglabel:SPECIFY AN OUTGROUP?
argtype:chooser
argchoice:Yes:Y
argchoice:No:N
argvalue:1

arg:OUTGRP
arglabel:SEQUENCE # OF OUTGROUP:
argtype:slider
argmin:1
argmax:1000
argvalue:1

arg:USERTREE
argtype:chooser
argchoice:Search for best tree:N
argchoice:Evaluate user-supplied tree:Y
argvalue:0

arg:UFN
arglabel:User tree filename:
argtype:text
argtext:none

arg:PREEDIT
arglabel:EDIT THE DATA BEFORE RUNNING fastDNAml?
argtype:chooser
argchoice:Yes:$GDE_TEXTEDIT in1.infile;
argchoice:No:
argvalue:1

arg:HOST
arglabel:Run program
argtype:chooser
argchoice:Locally:l
argchoice:On remote host:r
argvalue:0

arg:WHERE
arglabel:WHERE TO SEND OUTPUT
argtype:chooser
argchoice:Treetool:($GDE_TEXTEDIT in1.outfile; rm in1.outfile)& (treetool in1.treefile) & ($GDE_TEXTEDIT in1.treefile; rm in1.treefile) &  (if test -f in1.raw.treefile; then ($GDE_TEXTEDIT in1.raw.treefile; rm in1.raw.treefile)& fi)
argchoice:Drawtree:($GDE_TEXTEDIT in1.outfile; rm in1.outfile)& (mkdir in1.dir; cp in1.treefile in1.dir/treefile; cd in1.dir; cp $DAT/Phylip/font1 fontfile; drawtree.csh l r 0 360 360 yes 0.2 0.14286 |drawtree; $GDE_PSVIEW plotfile; cd ..; rm -r in1.dir) & ($GDE_TEXTEDIT in1.treefile; rm in1.treefile)& (if test -s in1.raw.treefile; then ($GDE_TEXTEDIT in1.raw.treefile; rm in1.raw.treefile)& fi)
argchoice:Output files:mv in1.outfile $OUTNAME.outfile; mv in1.treefile $OUTNAME.treefile; (if test -f in1.raw.treefile; then (mv in1.raw.treefile $OUTNAME.raw.treefile)& fi); echo "fastDNAml $OUTNAME completed" | mail -s fastDNAml_in1 `whoami`
argvalue:0
 
arg:OUTNAME
arglabel:raw name
argtype:text

in:in1
informat:genbank
insave:

