#------------------------- DNAML (11/ 1/2009)  --------------------------
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 $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

# biolegato: If no file has been chosen for UFN, UFN will be blank.
# Simply substituting $UFN into the command for dnaml.csh would
# therefore result in a missing parameter. Here we concatenate
# UTREE and UFN in the form UTREE_UFN. dnaml.csh has been
# modified to read both parameters from the UTREE variable,
# and UFN is no longer passed as a separate variable.  
arg:UTREE
argtype:chooser
argchoice:Search for best tree:n_$UFN
argchoice:Evaluate user-supplied tree:y_$UFN
argvalue:0

arg:UFN
arglabel:_____User tree filename:
argtype:text
#@argtype:file_chooser
argtext:none

arg: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: