name        "SeqKit stats - simple statistics on sequencing read files"
tip    "SeqKit stats - simple statistics on sequencing read files"
       
var "in1"
    type        tempfile
    direction   in
    format      tsv
    save        true

var "threads"
    type        number
    label       "Number of threads to use"
    min         1
    max         $BL_CORES_MAX
    default     $BL_CORES_DEFAULT

var "email"
    type        chooser
    label       "Notify of completion by email"
    default     1
    choices
        "Yes" "bl_email.py --recipient %ADDRESS% --subject 'SeqKit stats completed' --message %in1%.tsv;"
        "No" ""

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

panel
    var "Run"
        type        button
        label       "Run"
        shell       "bltsv2name.py %in1% %in1%.nam; FILES=`cat %in1%.nam`; seqkit stats -j %THREADS% -o %in1%.out $FILES; cat %in1%.out | tr -s ' ' | tr ' ' '\t' > %in1%.tsv; rm %in1%.nam; %EMAIL% blreads -noautonames %in1%.tsv"
        close       true
    var "Help"
        type        button
        label       "Help"
        shell       "chooseviewer.py $BIRCH/doc/seqkit.help"
        close       false