name        "gff2gtf - Create GTF file from a GFF file using gffread"
icon    "$BIRCH/dat/blreads/CCBlogo.png"
tip    "Convert a GFF file to a GTF file using gffread."

var "GFFFILE"
    type        file
    label       "GFF file (.gff/.gff3)"
    default     ""

var "NONTRANSCRIPT"
    type        chooser
    label       "Process non-transcript features?"
    default     1
    choices
        "Yes" "-O"
        "No" ""

var "INFRAMESTOP"
    type        chooser
    label       "Discard CDSs with in-frame stop codons?"
    default     1
    choices
        "Yes" "-V"
        "No" ""

var "NOPSEUDO"
    type        chooser
    label       "Filter out records matching the 'pseudo' keyword?"
    default     1
    choices
        "Yes" "--no-pseudo"
        "No" ""

var "ADDITIONAL"
    type        chooser
    label       "Move additional exon attributes to the mRNA level?"
    default     1
    choices
        "Yes" "-G"
        "No" ""

panel
    var "Run"
        type        button
        label       "Run"
        shell       "gff2gtf.py %GFFFILE% %NONTRANSCRIPT% %INFRAMESTOP% %NOPSEUDO% %ADDITIONAL%; blreads& "
        close       true

    var "Help"
        type        button
        label       "Help"
        shell       "$BIRCH/script/chooseviewer.py $BIRCH/doc/ccb/gffread.man"
        close       false