name    "DNADIST - DNA Distance methods"
icon    "$BIRCH/dat/blnalign/PCD/Phylogeny/phylip.gif"
tip     "DNA phylogenies using distance matrix methods"

var "in1"
    type        tempfile
    direction   in
    format      fasta
    save        true

var "dmethod"
    type        combobox
    label       "DISTANCE MATRIX METHOD"
    default     0
    choices
        "F84"       "f"
        "Kimura 2-parameter" "k"
        "Jukes-Cantor" "j"
        "Log of the determinant" "l"

var "transratio"
    type        number
    label       "TRANSITION/TRANSVERSION RATIO"
    min         1
    max         20
    default     2

var "method"
    type        combobox
    label       "RESAMPLING (SLOW!)"
    default     0
    choices
        "none"      "n"
        "Bootstrap" "b"
        "Delete-half jackinfe" "d"
        "Permute species for each character" "ps"
        "Permute character order" "po"
        "Permute within species" "pw"

var "replicates"
    type        number
    label       "_____Number of bootstrap replicates?"
    min         1
    max         1000
    default     100

var "blocksize"
    type        number
    label       "_____Block size (Bootstrap only)"
    min         1
    max         50
    default     1
var "percent"
    type        number
    label       "_____Percent of sites to sample"
    min         1
    max         100
    default     100

var "tconmeth"
    type        combobox
    label       "TREE CONSTRUCTION METHOD"
    default     0
    choices
        "Weighbor, weighted Neighbor Joining" "w"
        "FITCH, Fitch-Margoliash" "F"
        "FITCH, Minimum Evolution" "f"
        "KITSCH, Fitch-Margoliash constant evolutionary clock" "K"
        "KITSCH, Minimum Evolution constant evolutionary clock" "k"
        "Neighbor Joining" "N"
        "UPGMA"     "U"

var "power"
    type        text
    label       "POWER (FITCH,KITCH only)"
    default     "2.0"

var "negbranch"
    type        chooser
    label       "ALLOW NEGATIVE BRANCH LENGTHS? (FITCH,KITCH only)"
    default     1
    choices
        "Yes"       "y"
        "No"        "n"

var "outgrp"
    type        number
    label       "SEQUENCE # OF OUTGROUP:"
    min         1
    max         1000
    default     1

var "subrep"
    type        chooser
    label       "DO SUBREPLICATES?"
    default     0
    choices
        "Yes"       "y"
        "No"        "n"

var "global"
    type        chooser
    label       "DO GLOBAL REARRANGEMENTS?  (FITCH,KITCH only)"
    default     0
    choices
        "Yes"       "y"
        "No"        "n"

var "jumble"
    type        chooser
    label       "JUMBLE THE SEQUENCE ORDER?"
    default     0
    choices
        "Yes"       "J"
        "No"        "n"

var "numjum"
    type        number
    label       "_____Number of times to jumble"
    min         1
    max         50
    default     1

var "termout"
    type        chooser
    label       "SHOW PROGRESS REPORT"
    default     0
    choices
        "none"      "/dev/null"
        "on screen" "/dev/tty"
        "to .log file" "../../%OUTNAME%.log"

var "alltrees"
    type        chooser
    label       "Save raw trees to a separate file?"
    default     1
    choices
        "Yes"       "y"
        "No"        "n"

var "printdata"
    type        chooser
    label       "PRINT SEQUENCE DATA TO OUTFILE?"
    default     1
    choices
        "Yes"       "y"
        "No"        "n"

var "where"
    type        chooser
    label       "WHERE TO SEND OUTPUT"
    default     0
    choices
        "Tree editor" "bltreeoutput.py -e %in1%.outtree %in1%.outfile %OUTNAME%"
        "Drawing program" "bltreeoutput.py -d %in1%.outtree %in1%.outfile %OUTNAME%"
        "Output files" "bltreeoutput.py -f %in1%.outtree %in1%.outfile %OUTNAME%"

var "outname"
    type        text
    label       "_____raw filename (no extension)"
    default     "dnadist"

panel

    var "Run"
        type        button
        label       "Run"
        shell       "cat %in1% | sed ""s/[\:\_]CDS/_/"" > %in1%.infile; rm %in1%;  dnadist.py %in1%.infile %DMETHOD% %TRANSRATIO% %METHOD% %REPLICATES% %BLOCKSIZE% %PERCENT% %TCONMETH% %POWER% %SUBREP% %GLOBAL% %NEGBRANCH% %OUTGRP% %JUMBLE% %NUMJUM% %TERMOUT% %ALLTREES% %PRINTDATA% %in1%.outfile %in1%.outtree %in1%.outtree.alltrees; %WHERE%; rm %in1%.infile "
        close       true

    var "Help"
        type        button
        label       "Help"
        shell       "$BIRCH/script/chooseviewer.py $BIRCH/doc/Phylip/dnadist.html"
        close       false