// this menu defines windows for two PHYML interfaces: nucleotide and protein
// (depending on whether PHYML_NUC is defined or not)

#ifdef PHYML_NUC
# define SEQTYPE_NAME nucleotide
# define SEQTYPE_SHRT NUC
#else
# define SEQTYPE_NAME protein
# define SEQTYPE_SHRT PRO
#endif



// test for "no tree" below has to match ../../TEMPLATES/arb_global_defs.h@NO_TREE_SELECTED

#define PHYML_CALL(seqtype) \
        (   GOTO_LOCAL_DIR;GEN_PHYLIP(infile) && \
            RUN_IN_WINDOW(if [ "$TREE" != "tree_?????" -a ! -z "$TREE" ]; then arb_export_tree $TREE > input_tree.in; INPUT_TREE_PARAM=-uinput_tree.in; fi; \
                          ($ARBHOME/bin/phyml_20130708 \
                          --input=infile \
                          --datatype=seqtype \
                          --model=$MODEL \
                          -f$BASEFREQEST \
                          --bootstrap=$BOOTSTRAP \
                          --search=$SEARCH \
                          -o$PARAM_OPTIMIZATION \
                          --r_seed=$RAND_SEED \
                          --pinv=$PROPINVAR \
                          --alpha=$ALPHA \
                          $INPUT_TREE_PARAM \
                          $CUSTOM_PARAMS || STOP_ON_FAILURE(phyml_20130708)) &&  \
                          mv infile_phyml_tree.txt outtree && \
                          $DISPLAY_FUNC))&

item: PHYML-20130708 (SEQTYPE_NAME)
#ifdef PHYML_NUC
        seqtype: N
        itemmethod:PHYML_CALL(nt)
        itemmeta: P
#else
        seqtype: A
        itemmethod:PHYML_CALL(aa)
        itemmeta: Y
#endif
itemhelp:phyml-20130708.help

// $INPUT_TREE_PARAM is either empty or contains -uinput_tree.in depending on the selection of the starting tree


arg:DISPLAY_FUNC
argtype:choice_menu
arglabel:What to do with the tree?
argchoice:ARB ('tree_phyml_'):arb_read_tree tree_phyml_$$ outtree "PRG=phyml-20130708 FILTER=$FILTER STYPE=SEQTYPE_SHRT"
argchoice:TextEdit:arb_textedit outfile
argchoice:Treetool:treetool outtree


arg:MODEL
argtype:choice_menu
arglabel:Nuc. substitution model
#ifdef PHYML_NUC
        argchoice:GTR:GTR
        argchoice:HKY85 (default):HKY85
        argchoice:JC69:JC69
        argchoice:K80:K80
        argchoice:F81:F81
        argchoice:F84:F84
        argchoice:TN93:TN93
#else
        argchoice:LG (default):LG
        argchoice:WAG:WAG
        argchoice:JTT:JTT
        argchoice:MtREV:MtREV
        argchoice:Dayhoff:Dayhoff
        argchoice:DCMut:DCMut
        argchoice:RtREV:RtREV
        argchoice:CpREV:CpREV
        argchoice:VT:VT
        argchoice:Blosum62:Blosum62
        argchoice:MtMam:MtMam
        argchoice:MtArt:MtArt
        argchoice:HIVw:HIVw
        argchoice:HIVb:HIVb
#endif

arg:PARAM_OPTIMIZATION
argtype:choice_menu
arglabel:Specific parameter optimization
argchoice:Optimize tree topology, branch len, rate params:tlr
argchoice:Optimize tree topology and branch length:tl
argchoice:Optimize branch length and rate parameters:lr
argchoice:Optimize branch length:l
argchoice:Optimize rate parameters:r
argchoice:Do not optimize any parameters:n

arg:PROPINVAR
argtype:text
arglabel:Proportion of invariable sites\n(Range [0..1] or e to get the maximum likelihood estimate)
argtext:e

arg:ALPHA
argtype:text
arglabel:Distribution of the gamma distribution shape parameter\n(Positive value or e to get the maximum likelihood estimate)
argtext:e

arg:RAND_SEED
argtype:text
arglabel:Pseudo random number generator seed
argtext:424242

arg:BASEFREQEST
argtype:choice_menu
arglabel:Base frequency estimates
argchoice:Empirical:e
#ifdef PHYML_NUC
        argchoice:ML:m
#else
        argchoice:Model:m
#endif

arg:BOOTSTRAP
arglabel:Bootstrap
argtype:choice_menu
argchoice:(default) approximate Bayes branch supports:-5
argchoice:neither approximate likelihood ratio test nor bootstrap values are computed:0
argchoice:approximate likelihood ratio test returning aLRT statistics:-1
argchoice:approximate likelihood ratio test returning Chi2-based parametric branch supports:-2
argchoice:SH-like branch supports alone:-4
argchoice:20 bootstrap replicates:20
argchoice:50 bootstrap replicates:50
argchoice:100 bootstrap replicates:100
argchoice:200 bootstrap replicates:200
argchoice:500 bootstrap replicates:500
argchoice:1000 bootstrap replicates:1000
argchoice:10000 bootstrap replicates:10000

arg:SEARCH
argtype:choice_menu
arglabel:Tree topology search operation option
argchoice:NNI (default, fast):NNI
argchoice:SPR (a bit slower than NNI):SPR
argchoice:BEST (best of NNI and SPR search):BEST

arg:TREE
argtype:tree
arglabel:Starting tree
argchoice:?????

arg:CUSTOM_PARAMS
argtype:text
arglabel: Custom parameters
argtext:

in:TmpInputFile
informat:genbank
insave: