#-------------------- Discrete data distance methods  (11/ 4/2009) ------------------
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 $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
 
# 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: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: