#-------------------- Discrete data - RESTML  (11/ 4/2009) ------------------
item: RFLP/RAPD/AFLP Max. Likelihood
itemmethod:flat2phyl -s <in1 > in1.tmp; rm in1; (restml.csh in1.tmp $UTREE $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
 
# mbiolegato: If no file has been chosen for UFN, UFN will be blank.
# Simply substituting $UFN into the command for restml.csh would
# therefore result in a missing parameter. Here we concatenate
# UTREE and UFN in the form UTREE_UFN. restml.csh has been
# modified to read both parameters from the UTREE variable,
# and UFN is no longer passed as a separate variable.  
arg:UTREE
argtype:chooser
argchoice:Search for best tree:n_$UFN
argchoice:Evaluate user-supplied tree:y_$UFN
argvalue:0

arg:UFN
arglabel:_____User tree filename:
argtype:text
#@argtype:file_chooser
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# variable $SPEEDY in the itemmethod has been replaced by 'n'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