name    "fixfq.py - Separate valid reads and bad reads into two files"
icon    "$BIRCH/public_html/images/birch_black_ico.png"
tip    "For each selected fastq file, divides the reads from a fastq file into two files, one for valid reads (validfile) and the other for bad reads (badfile)"
       
var "in1"
    type        tempfile
    direction   in
    format      tsv
    save        false

var "minseq"
    type        number
    label       "Min. length of a valid read"
    min         1
    max         500000000
    default     50

var "out1"
    type        tempfile
    direction   out
    format      tsv
    save        false
    overwrite   true
    content     canvas

var "output"
    type        chooser
    label       "Notify of completion by email"
    default     1
    choices
        "Yes" "bl_email.py --recipient %ADDRESS% --subject 'fixfq.py completed' --message fixfq.log;"
        "No" "chooseviewer.py fixfq.log;"

var "address"
    type        text
    label       "    email address"
    default     "$BL_EMAIL"

panel
    var "Run"
        type        button
        label       "Run"
        shell       "bltsv2name.py %in1% %in1%.tsv; fixfq.py --filelist %in1%.tsv --minseq %MINSEQ% > fixfq.log; rm %in1%.tsv; %OUTPUT% bldirtab.py %out1%"
        close       true

    var "Manual"
        type        button
        label       "Manual"
        shell       "chooseviewer.py $BIRCH/doc/fixfq.html"
        close       false