name        "Pollux - DNA read correction (k-mer)"
tip    "Corrects DNA sequencing reads based on k-mer frequencies. Works for all sequencing platforms. "
       
var "in1"
    type        tempfile
    direction   in
    format      tsv
    save        false

var "paired"
    type        chooser
    label       "Paired-end reads?"
    default     0
    choices
        "Yes (default)" "-p"
        "No" ""

var "klength"
    type        number
    label       "k-mer length"
    min         16
    max         31
    default     31

# The author mentions this in the paper, but we'll have to experiment
# to find out how pollux wants us to specify "size eg. # nucleotides, 
# RAM in byes, RAM in Mb or Gb etc.
#var "batch"
#    type        combobox
#    label       "limit RAM: # bases processed at a time"
#    default     0
#    choices
#        "off (default)" ""
#        "200,000,000" "200000000"
#        "250,000,000" "-b 250000000"
#        "30 Gb" "-b 30"
#        "30000 Mb" "-b 30000"

var "fastqc"
    type        chooser
    label       "Run FASTQC on corrected reads?"
    default     0
    choices
        "Yes" "FILES=`cat %in1%.nam | sed -e 's/$/.corrected/'`; echo 'FASTQC Start: '`date` >> pollux.log; fastqc -t %THREADS% $FILES >> pollux.log; echo 'FASTQC Finish: '`date` >> pollux.log; rm %in1%.nam;"
        "No (default)" ""

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

var "outdir"
    type        text
    label       "Name for output directory"
    default     "../pollux"

var "email"
    type        chooser
    label       "Notify of completion by email"
    default     1
    choices
        "Yes" "bl_email.py --recipient %ADDRESS% --subject 'pollux completed' --message pollux.log;"
        "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 |tr '\n' ' '` ; mkdir %OUTDIR%; echo 'Start: '`date` > pollux.log; nice pollux %PAIRED% -k %KLENGTH% -o %OUTDIR% -i $FILES >> pollux.log; echo 'Finish: '`date` >> pollux.log; mv pollux.log %in1%.nam %OUTDIR%; cd %OUTDIR%; %FASTQC% %EMAIL% blreads "
        shell       "mkdir %OUTDIR%; echo 'Start: '`date` > pollux.log; bl_pollux.sh %in1% %OUTDIR% %PAIRED% -k %KLENGTH% ; RCODE=$?; echo 'Finish: '`date` >> pollux.log; if [ $RCODE -eq '0' ]; then (mv pollux.log %OUTDIR%; cd %OUTDIR%; %FASTQC% %EMAIL% blreads) fi "

        close       true
    var "Help"
        type        button
        label       "Help"
        shell       "chooseviewer.py $BIRCH/doc/pollux.man"
        close       false