name        "PRIMER 3"
tip    "construct PCR primers and oligos"
tabset
    tab "PCR primers"
        var "maxprimers"
            type        number
            label       "Find the N best primer pairs/internal oligos (N):"
            min         1
            max         30
            default     5
        var "optlen"
            type        number
            label       "optimal    PRIMER LENGTH"
            min         10
            max         50
            default     20
        var "minlen"
            type        number
            label       "minimum    PRIMER LENGTH"
            min         10
            max         50
            default     18
        var "maxlen"
            type        number
            label       "maximum    PRIMER LENGTH"
            min         10
            max         50
            default     22
        var "opttemp"
            type        number
            label       "optimal    PRIMER Tm"
            min         30
            max         100
            default     60
        var "mintemp"
            type        number
            label       "minimum    PRIMER Tm"
            min         30
            max         100
            default     57
        var "maxtemp"
            type        number
            label       "maximum    PRIMER Tm"
            min         30
            max         100
            default     63
        var "mingc"
            type        number
            label       "minimum    %GC"
            min         20
            max         80
            default     20
        var "maxgc"
            type        number
            label       "maximum    %GC"
            min         20
            max         80
            default     80
        var "saltconc"
            type        number
            label       "SALT concentration (mM)"
            min         10
            max         500
            default     50
        var "dnaconc"
            type        number
            label       "DNA   concentration (nM)"
            min         1
            max         100
            default     50
        var "maxunk"
            type        number
            label       "maximum UNKNOWN BASES (Ns) allowed in primer"
            min         0
            max         5
            default     0
        var "maxself"
            type        number
            label       "maximum primer SELF-COMPLEMENTARITY"
            min         0
            max         20
            default     12
        var "max3pself"
            type        number
            label       "maximum primer 3' END SELF-COMPLEMENTARITY"
            min         0
            max         20
            default     8
        var "gcclamp"
            type        number
            label       "GC CLAMP (how many 3' bases?)"
            min         0
            max         5
            default     0
        var "minprod"
            type        number
            label       "minimum PRODUCT LENGTH"
            min         100
            max         3000
            default     100
        var "maxprod"
            type        number
            label       "maximum PRODUCT LENGTH"
            min         100
            max         3000
            default     500
        var "target"
            type        chooser
            label       "--------- Find primers flanking a target sequence? ---------"
            default     1
            choices
                "Yes"       "1"
                "No"        "0"
        var "targetstart"
            type        number
            label       "Target start site"
            min         1
            max         500000
            default     1
        var "targetend"
            type        number
            label       "Target end site"
            min         1
            max         500000
            default     500000


    tab "Internal oligo"
        var "intoligo"
            type        chooser
            label       "===========FIND AN OLIGO INTERNAL TO PCR FRAGMENT?========"
            default     1
            choices
                "Yes"       "1"
                "No"        "0"
        var "ioptlen"
            type        number
            label       "optimal    OLIGO LENGTH"
            min         10
            max         50
            default     20
        var "iminlen"
            type        number
            label       "minimum    OLIGO LENGTH"
            min         10
            max         50
            default     18
        var "imaxlen"
            type        number
            label       "maximum    OLIGO LENGTH"
            min         10
            max         50
            default     27
        var "iopttemp"
            type        number
            label       "optimal    OLIGO Tm"
            min         30
            max         100
            default     60
        var "imintemp"
            type        number
            label       "minimum    OLIGO Tm"
            min         30
            max         100
            default     57
        var "imaxtemp"
            type        number
            label       "maximum    OLIGO Tm"
            min         30
            max         100
            default     63
        var "imingc"
            type        number
            label       "minimum    %GC"
            min         20
            max         80
            default     20
        var "imaxgc"
            type        number
            label       "maximum    %GC"
            min         20
            max         80
            default     80
        var "isaltconc"
            type        number
            label       "SALT concentration (mM)"
            min         10
            max         500
            default     50
        var "idnaconc"
            type        number
            label       "DNA   concentration (nM)"
            min         1
            max         100
            default     50
        var "imaxunk"
            type        number
            label       "maximum UNKNOWN BASES (Ns) allowed in OLIGO"
            min         0
            max         5
            default     0
        var "imaxself"
            type        number
            label       "maximum OLIGO SELF-COMPLEMENTARITY"
            min         0
            max         20
            default     12
        var "in1"
            type        tempfile
            direction   in
            format      flat
            save        true
        var "imax3pself"
            type        number
            label       "maximum OLIGO 3' END SELF-COMPLEMENTARITY"
            min         0
            max         20
            default     12
panel
    var "Run"
        type        button
        label       "Run"
        shell       "primer3b.py %in1% %MAXPRIMERS% %OPTLEN% %MINLEN% %MAXLEN% %OPTTEMP% %MINTEMP% %MAXTEMP% %MINGC% %MAXGC% %SALTCONC% %DNACONC% %MAXUNK% %MAXSELF% %MAX3PSELF% %GCCLAMP% %MINPROD% %MAXPROD% %TARGET% %TARGETSTART% %TARGETEND% %intoligo% %ioptlen% %iminlen% %imaxlen% %iopttemp% %imintemp% %imaxtemp% %imingc% %imaxgc% %isaltconc% %idnaconc% %imaxunk% %imaxself% %imax3pself% > %in1%.in; nedit %in1%.in; $RM_CMD %in1%; primer3brun.py %in1%.in"
        close       true
    var "Help"
        type        button
        label       "Help"
        shell       "chooseviewer.py $BIRCH/doc/primer/primer3_manual.htm"
        close       false