# .GDEmenus for Solaris-Sparc 
# 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   1/7/2006  by Brian Fristensky                 #
#                                                                          #
############################################################################


#
####################################################################
# This file creates menus for mgde, a client program for working with
# discrete data eg. molecular markers.
####################################################################


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

#-------------------------------- New marker set ----------------------------
item:New marker set   <meta N>
itemmethod:echo '"$NAME' > out1
itemmeta:n
itemhelp:doc/GDE/new_sequence.help
itemopen:gde_help_viewer.csh
 
arg:NAME 
argtype:text 
arglabel:New dataset name? 
argtext:New 
 
out:out1
outformat:flat

#---------------- Import Phylip Discrete Data  (3/12/97) -------------------
item:Import Phylip Discrete Data
itemmethod:phyl2flat $FILETYPE < $INPUTFILE > out1
itemhelp:
itemopen:gde_help_viewer.csh

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

arg:FILETYPE
argtype:chooser
arglabel:Phylip file format
argchoice:interleaved:
argchoice:non-interleaved:-n
argvalue:0

out:out1
outformat:flat

#---------------- Import Discrete Data from CSV file (4/26/2008) -------------------
item:Import Discrete Data from CSV file
itemmethod:cat $INPUTFILE | csv2phyl.sh | phyl2flat > out1
itemhelp:doc/mGDE/ImportCSV.help
itemopen:gde_help_viewer.csh

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

out:out1
outformat:flat

#---------------- Export Phylip Discrete Data  (1/ 8/96) -------------------
item:Export Phylip Discrete Data
itemmethod:flat2phyl < in1 > $OUTPUTFILE;$RM_CMD in1
itemhelp:
itemopen:gde_help_viewer.csh

arg:OUTPUTFILE
argtype:text
#argtype:file_chooser
arglabel:Name of file?

in:in1
informat:flat
insave:

#-------------------------------- Save selection 1/7/06 --------------------------
item:Save Selection
itemmethod: $SAVE_FUNC 
itemhelp:doc/GDE/save_selection.help
itemopen:gde_help_viewer.csh

arg:SAVE_FUNC
argtype:chooser
arglabel:File format
argchoice:Flat:cat in1 > $OUTNAME
argchoice:Phylip discrete data:flat2phyl < in2 > $OUTNAME
argchoice:GDE:cat in3 > $OUTNAME
argvalue:2

arg:OUTNAME
argtype:text
arglabel:File name?

in:in1
informat:flat

in:in2
informat:flat

in:in3
informat:gde


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

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


item:ViewDocumentation
itemmethod:($DOCUMENT)&

arg:DOCUMENT
arglabel:Documentation file
argtype:choice_menu
argchoice:GDE Documentation:$birch/script/browser.csh $tutorials/GDE/gde.html
argchoice:mGDE Interface Documentation:$birch/script/browser.csh $tutorials/GDE/overview/GDE.interfaces.html#mGDE
argchoice:GDE Manual:$GDE_PDFVIEW $DOC/GDE/GDE2.2_manual.pdf
argchoice:Phylip Main Document:$birch/script/browser.csh $DOC/Phylip/main.html
argchoice:Phylip Discrete Data:$birch/script/browser.csh $DOC/Phylip/discrete.html
argvalue:0


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

# -------------------------------   sort    --------------------------------
item:Sort
itemmethod:(heapsortHGL in1 $PRIM_KEY $SEC_KEY > in1.tmp ; mgde in1.tmp;$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 ( 4/ 7/06)  ----------------------------
item:Copy out
itemmethod:sed -e "s/^LOCUS   /LOCUS/" -e "s/^ ACCESSION/ACCESSION /" -e "/^$/d"  in1 > $HOME/.mGDEclipboard

in:in1
informat:genbank

# ----------------------- Paste in  4/ 7/06) ----------------------------
item:Paste in
itemmethod:cp $HOME/.mGDEclipboard out1

out:out1
outformat:genbank

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

in:in1
informat:gde
insave:



############################## 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

#-------------------- Discrete data distance methods  (12/ 3/2007) ------------------
item: RFLP/RAPD/AFLP etc. Distance methods
itemmethod:flat2phyl <in1 > in1.tmp; rm in1; (restdist.csh in1.tmp $MODEL $TRANSRATIO $SITELEN $METHOD $BSEED $REPLICATES $PERCENT $TCONMETH $POWER $SUBREP $GLOBAL $NEGBRANCH $OUTGRP $JUMBLE $JSEED $NUMJUM $TERMOUT $PRINTDATA  in1.outfile in1.outtree; rm in1.tmp; $WHERE) &
itemhelp:doc/Phylip/distance.html
itemopen:gde_help_viewer.csh
 
arg:MODEL
argtype:choice_menu
arglabel:DISTANCE MODEL
argchoice:SITES- modified DNA change model (Nei/Li):S
argchoice:SITES- original DNA change model (Nei/Li):s
argchoice:REST. FRAGS- modified DNA change model (Nei/Li):R
argchoice:REST. FRAGS- original DNA change model (Nei/Li):r
argvalue:0

arg:TRANSRATIO
arglabel:TRANSITION/TRANSVERSION RATIO (Mod. Nei/Li ONLY)
argtype:slider
argmin:1
argmax:20
argvalue:2

arg:SITELEN
arglabel:SITE LENGTH
argtype:slider
argmin:1
argmax:50
argvalue:6

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: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: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:restdist

in:in1
informat:flat

#-------------------- Discrete data distance methods  ( 1/30/2007) ------------------
item: RFLP/RAPD/AFLP etc. Parsimony
#itemmethod:flat2phyl -s <in1 > in1.tmp; rm in1; (discpars.csh in1.tmp $UTREE $UFN $METHOD $BSEED $REPLICATES $PERCENT $TCONMETH $PARSTYPE $THRESHOLD $OUTGRP $JUMBLE $JSEED $NUMJUM $TERMOUT $ALLTREES  in1.outfile in1.outtree in1.outtree.alltrees; rm in1.tmp; $WHERE) &
itemmethod:(discpars.csh in1 $UTREE $UFN $METHOD $BSEED $REPLICATES $PERCENT $TCONMETH $PARSTYPE $THRESHOLD $OUTGRP $JUMBLE $JSEED $NUMJUM $TERMOUT $ALLTREES  in1.outfile in1.outtree in1.outtree.alltrees; rm in1; $WHERE) &
itemhelp:doc/Phylip/discrete.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: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:PERCENT
argtype:slider
arglabel:_____Percent of sites to sample
argmin:1
argmax:100
argvalue:100

arg:TCONMETH
arglabel:PARSIMONY METHOD
argtype:choice_menu
argchoice:DOLLOP -  Dollo:d
argchoice:DOLLOP -  Polymorphism:p
argchoice:MIX -  Camin-Sokal:c
argchoice:MIX -  Wagner:w
#argchoice:MIX -  mixed Wagner and Camin-Sokol:x
argchoice:PARS - rearrange multiple trees:P
argchoice:PARS - collapse unchanged branches:L
argchoice:PARS - rearrange only on best tree:1
argvalue:0

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

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:ALLTREES
argtype:chooser
arglabel:Save raw trees to a separate file?
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:discpars

in:in1
informat:flat
insave:

#-------------------- Discrete data - RESTML  ( 8/24/2007) ------------------
item: RFLP/RAPD/AFLP Max. Likelihood
itemmethod:flat2phyl -s <in1 > in1.tmp; rm in1; (restml.csh in1.tmp $UTREE $UFN $METHOD $BSEED $REPLICATES $PERCENT $ALLSITES n $GLOBAL $SITENUM $SITELEN $OUTGRP $JUMBLE $JSEED $NUMJUM $TERMOUT $PRINTDATA  in1.outfile in1.outtree; rm in1.tmp; $WHERE) &
itemhelp:doc/Phylip/restml.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: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:PERCENT
argtype:slider
arglabel:_____Percent of sites to sample
argmin:1
argmax:100
argvalue:100

arg:ALLSITES
arglabel:ARE ALL SITES DETECTED?
argtype:chooser
argchoice:Yes:y
argchoice:No:n
argvalue:1

# As of Phylip 3.63, there is a bug in RESTML that causes the program
# to hang while adding species to a tree. This only occurs when
# Speedier but rougher analysis is set to 'yes'. Therefore, the
# variable $SPEEDY in the itemmethod has been replaced by 'n'
# and this option will remain commmented out until RESTML is fixed.
#arg:SPEEDY
#arglabel:SPEEDIER BUT ROUGHER ANALYSIS?
#argtype:chooser
#argchoice:Yes:y
#argchoice:No:n
#argvalue:1

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

arg:SITENUM
arglabel:# of rest. enzymes (RFLP only)
argtype:slider
argmin:1
argmax:100
argvalue:1

arg:SITELEN
arglabel:SITE LENGTH
argtype:slider
argmin:1
argmax:50
argvalue:6

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

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:restml

in:in1
informat:flat

#-------------------- Discrete data distance methods  ( 7/ 7/2006) ------------------
item: (test) RFLP/RAPD/AFLP etc. Parsimony
itemmethod:flat2phyl -s <in1 > in1.tmp; rm in1; (discpars.test.csh in1.tmp $UTREE $UFN $METHOD $BSEED $REPLICATES $PERCENT $TCONMETH $PARSTYPE $THRESHOLD $OUTGRP $JUMBLE $JSEED $NUMJUM $TERMOUT $PRINTDATA  in1.outfile in1.outtree; rm in1.tmp; $WHERE) &
itemhelp:doc/Phylip/discrete.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: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:PERCENT
argtype:slider
arglabel:_____Percent of sites to sample
argmin:1
argmax:100
argvalue:100

arg:TCONMETH
arglabel:PARSIMONY METHOD
argtype:choice_menu
argchoice:DOLLOP -  Dollo:d
argchoice:DOLLOP -  Polymorphism:p
argchoice:MIX -  Camin-Sokal:c
argchoice:MIX -  Wagner:w
#argchoice:MIX -  mixed Wagner and Camin-Sokol:x
argvalue:0

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

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:discpars

in:in1
informat:flat

#-------------------- Discrete data - RESTML  ( 8/27/2007) ------------------
item: (test)RFLP/RAPD/AFLP Max. Likelihood
itemmethod:flat2phyl -s <in1 > in1.tmp; rm in1; (restml.test.csh in1.tmp $UTREE $UFN $METHOD $BSEED $REPLICATES $PERCENT $ALLSITES n $GLOBAL $SITENUM $SITELEN $OUTGRP $JUMBLE $JSEED $NUMJUM $TERMOUT $PRINTDATA  in1.outfile in1.outtree; rm in1.tmp; $WHERE) &
itemhelp:doc/Phylip/restml.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: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:PERCENT
argtype:slider
arglabel:_____Percent of sites to sample
argmin:1
argmax:100
argvalue:100

arg:ALLSITES
arglabel:ARE ALL SITES DETECTED?
argtype:chooser
argchoice:Yes:y
argchoice:No:n
argvalue:1

# As of Phylip 3.63, there is a bug in RESTML that causes the program
# to hang while adding species to a tree. This only occurs when
# Speedier but rougher analysis is set to 'yes'. Therefore, the
# variable $SPEEDY in the itemmethod has been replaced by 'n'
# and this option will remain commmented out until RESTML is fixed.
#arg:SPEEDY
#arglabel:SPEEDIER BUT ROUGHER ANALYSIS?
#argtype:chooser
#argchoice:Yes:y
#argchoice:No:n
#argvalue:1

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

arg:SITENUM
arglabel:# of rest. enzymes (RFLP only)
argtype:slider
argmin:1
argmax:100
argvalue:1

arg:SITELEN
arglabel:SITE LENGTH
argtype:slider
argmin:1
argmax:50
argvalue:6

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

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:restml

in:in1
informat:flat

