name        "Jalview - multiple sequence alignment"
icon    "$BIRCH/dat/birch/jalview_icon.png"
tip    "creation, analysis and visualization of multiple alignments"
var "in1"
    type        tempfile
    direction   in
    format      fasta
    save        true
panel
    var "Run"
        type        button
        label       "Run"
        shell       "(tr ""~"" ""-"" <%in1% | sed ""s/:.*//"" |sed ""s/\*//"" > %in1%.fsa; jalview -open $PWD/%in1%.fsa; sleep 100; rm %in1% %in1%.fsa)&"
        #shell       "(tr ""~"" ""-"" <%in1% | sed ""s/:.*//"" |sed ""s/\*//"" > %in1%.fsa; jalview $PWD/%in1%.fsa; sleep 100; rm %in1% %in1%.fsa)&"
        close       true
    var "Help"
        type        button
        label       "Help"
        shell       "$BIRCH/script/chooseviewer.py $BIRCH/doc/jalview/help.html"
        close       false