name        "gigaNUMSEQ - number a large sequence"
icon    "$BIRCH/public_html/images/birch_black_ico.png"
tip    "pretty-print and translate sequences up to 5e8 bp. Used for printing sequences from chromosomes."

#Max. seq. length is based on NZ_ABJB000000000 (Ixodes scapularis), currently the largest
# sequence in GenBank, at 895,741,386 bp.
# Modifying the C-code for numseq to take a sequence larger than 500,000,000 causes a
# truncation error upon compilation. Until that problem can be solved, the maximum
# sequence is 500,000,000

var "start"
    type        number
    label       "START"
    min         1
    max         500000000
    default     1
var "finish"
    type        number
    label       "FINISH"
    min         1
    max         500000000
    default     10000000
var "nuccase"
    type        chooser
    default     0
    choices
        "UPPERCASE" "U"
        "lowercase" "l"
var "snum"
    type        number
    label       "Number of starting nucleotide"
    min         -500000000
    max         500000000
    default     0
var "group"
    type        number
    label       "write in GROUPs of"
    min         1
    max         100
    default     10
var "gpl"
    type        number
    label       "number of GROUPs printed per line"
    min         1
    max         20
    default     7
var "which"
    type        chooser
    label       "Which strand?"
    default     0
    choices
        "original"  "i"
        "opposite"  "o"
var "strands"
    type        chooser
    default     0
    choices
        "One strand" "1"
        "Both strands" "2"
var "kind"
    type        chooser
    label       "Print as"
    default     0
    choices
        "DNA"       "D"
        "RNA"       "R"
var "numbers"
    type        chooser
    label       "Numbering"
    default     0
    choices
        "YES"       "Y"
        "NO"        "N"
var "nucs"
    type        chooser
    label       "Print nucleotides"
    default     0
    choices
        "YES"       "Y"
        "NO"        "N"
var "peptides"
    type        chooser
    label       "TRANSLATION"
    default     1
    choices
        "YES"       "Y"
        "NO"        "N"
var "frames"
    type        chooser
    label       "Reading frames"
    default     0
    choices
        "One"       "1"
        "Three"     "3"
var "form"
    type        chooser
    label       "aa code"
    default     1
    choices
        "Three letter" "L"
        "One letter" "S"
var "in1"
    type        tempfile
    direction   in
    format      genbank
    save        true
var "gcfile"
    type        combobox
    label       "Genetic Code"
    default     0
    choices
        "Standard"  "$BIRCH/dat/fsap/gc/1.standard.gc"
        "Vertebrate Mitochondrial" "$BIRCH/dat/fsap/gc/2.vert_mito.gc"
        "Yeast Mitochondrial" "$BIRCH/dat/fsap/gc/3.yeast_mito.gc"
        "Mold, Protozoan, and Coelenterate Mitochondrial" "$BIRCH/dat/fsap/gc/4.MPC.mito.gc"
        "Invertebrate Mitochondrial" "$BIRCH/dat/fsap/gc/5.inv_mito.gc"
        "Ciliate, Dasycladacean and Hexamita" "$BIRCH/dat/fsap/gc/6.CDH.gc"
        "Echinoderm and Flatworm" "$BIRCH/dat/fsap/gc/9.EF_mito.gc"
        "Euplotid"  "$BIRCH/dat/fsap/gc/10.Euplotid.gc"
        "Bacterial and Plant Plastid" "$BIRCH/dat/fsap/gc/11.Bact_Plastid.gc"
        "Alternative Yeast Nuclear" "$BIRCH/dat/fsap/gc/12.alt_yeast.gc"
        "Ascidian Mitochondrial" "$BIRCH/dat/fsap/gc/13.Ascidian_mito.gc"
        "Alternative Flatworm Mitochondrial" "$BIRCH/dat/fsap/gc/14.alt_flatworm_mito.gc"
        "Blepharisma" "$BIRCH/dat/fsap/gc/15.Blepharisma.gc"
        "Chlorophycean Mitochondrial" "$BIRCH/dat/fsap/gc/16.Chlorophycean_mito.gc"
        "Trematode Mitochondrial" "$BIRCH/dat/fsap/gc/21.Trematode_mito.gc"
        "Scenedesmus obliquus mitochondrial" "$BIRCH/dat/fsap/gc/22.Scenedesmus_mito.gc"
        "Thraustochytrium Mitochondrial" "$BIRCH/dat/fsap/gc/23.Thraustochytrium_mito.gc"
panel
    var "Run"
        type        button
        label       "Run"
        shell       "numseq.py %in1% %in1%.out %GCFILE% %START% %FINISH% %NUCCASE% %SNUM% %GROUP% %GPL% %WHICH% %STRANDS% %KIND% %NUMBERS% %NUCS% %PEPTIDES% %FRAMES% %FORM%; $RM_CMD %in1%; $BIRCH/script/chooseviewer.py %in1%.out; $RM_CMD %in1%*"
        close       true
    var "Help"
        type        button
        label       "Help"
        shell       "$BIRCH/script/chooseviewer.py $BIRCH/doc/fsap/numseq.txt"
        close       false