name        "transrate - de-novo transcriptome quality"
tip    "Analyse a de-novo transcriptome assembly using read-mapping data. NOTE: transrate cannot read compressed files (eg. .gz). Read files must be in FASTQ format."

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

var "assembly"
    type        file
    label       "Transcriptome assembly file (Fasta)"

var "reference"
    type        chooser
    label       "Compare to reference transcriptome (proteome)?"
    default     1
    choices
        "Yes" "--reference=%REFNAME%"
        "No" ""

var "refname"
    type        text
    label       "    reference filename"
    default     ""

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

var "outname"
    type        text
    label       "Name for output directory"
    default     "transrate"

var "OUTPUT"
    type        chooser
    label       "Notify of completion by email"
    default     1
    choices
        "Send output by email" "bl_email.py --recipient %ADDRESS% --subject 'transrate completed' --message transrate.log;"
        "Show output on screen" "($BL_TextEditor transrate.log)&  ($BL_Spreadsheet assemblies.csv)&"

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


panel
    var "Run"
        type        button
        label       "Run"
        shell       "echo 'Start: '`date` > transrate.log; OUTDIR=`dirname %ASSEMBLY%`/%OUTNAME%; bl_transrate.sh %in1% --assembly=%ASSEMBLY% %REFERENCE% --threads=%THREADS% --output=$OUTDIR  >> transrate.log; RCODE=$?; echo 'Finish: '`date` >> transrate.log; if [ $RCODE -eq '0' ]; then (mv transrate.log $OUTDIR; cd $OUTDIR; %OUTPUT%) fi"
#        shell       "echo 'Start: '`date` > transrate.log; OUTDIR=`dirname %ASSEMBLY%`/%OUTNAME%; echo 'OUTDIR: '${OUTDIR}; "
        close       true

    var "Help"
        type        button
        label       "Help"
        shell       "$BIRCH/script/chooseviewer.py $BIRCH/doc/pkg/transrate/transrate.man"
        close       false