name        "MaxAlign - Remove sequences that cause too many gaps"
icon    "$BIRCH/dat/blpalign/PCD/Alignment/DTU.png"
tip    "Maximizing the size of gap-free columns by selecting an optimal subset of sequences in an alignment"

var "charset"
    type        combobox
    label       "Character set "
    default     0
    choices
        "All characters valid (default)"        ""
        "Only 20 standard amino acids"        "--charset PROT"
        "20 standard amino acids, gaps are valid characters"        "--charset 'CDEFGHIKLMNPQRSTUVWY\-'"

var "heuristic"
    type        combobox
    label       "Heuristic "
    default     0
    choices
        "No synergy (-h=1, default)"        "--heuristic 1"
        "Synergy between 2 sets (-h=2, slow)"        "--heuristic 2"
        "Synergy between 3 sets (-h=3, very slow)"        "--heuristic 3"

var "remgaps"
    type        chooser
    label       "Remove columns in which all sequences have a gap"
    default     1
    choices
        "Yes"       "--remgaps"
        "No (default)"        ""

#var "OUTPUT"
#    type        chooser
#    label       "Where to send output"
#    default     0
#    choices
#        "Show output on screen" "(blpalign %in1%.fsa)& (chooseviewer.py %in1%.report.txt --delete)&  (chooseviewer.py %in1%.excluded.txt --delete)& (chooseviewer.py %in1%.retained.txt --delete)&"
#        "Send output to files" "mv %in1%.fsa %OUTNAME%.fsa; mv %in1%.report.txt %OUTNAME%.report.txt;mv %in1%.excluded.txt %OUTNAME%.excluded.txt; mv %in1%.retained.txt %OUTNAME%.retained.txt;"
#var "outname"
#    type        text
#    label       "     name for output files"
#    default     "maxalign"

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

panel
    var "Run"
        type        button
        label       "Run"
        # maxalign.py takes care of opening output files on the screen
        shell       "maxalign.py %REMGAPS% %HEURISTIC% %CHARSET% --seqtype pro %in1%"
        #shell       "maxalign.py %REMGAPS% %HEURISTIC% %CHARSET% %in1%; %OUTPUT%"
        close       true
    var "WebDocs"
        type        button
        label       "WebDocs"
        shell       "chooseviewer.py https://services.healthtech.dtu.dk/services/MaxAlign-1.2/"
        close       false
    var "Manual"
        type        button
        label       "Manual"
        shell       "chooseviewer.py $doc/maxalign/maxalign.help"
        close       false