name        "quast - Genome assembly quality report"
icon    "$BIRCH/pkg/spades/spades_only_sign.png"
tip    "Generates reports and statistics on quality of a genome assembly."

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

var "reference"
    type        chooser
    label       "Compare to reference genome?"
    default     1
    choices
        "Yes" "-R %REFNAME%"
        "No" ""

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

var "eukaryote"
    type        chooser
    label       "Is genome eukaryotic?"
    default     1
    choices
        "Yes" "--eukaryote"
        "No" ""

var "SCAFFOLDS"
    type        chooser
    label       "Are the assemblies scaffolds?"
    default     1
    choices
        "Yes" "--scaffolds"
        "No" ""

var "MEMORYEFFICIENT"
    type        chooser
    label       "Conserve memory? (slow)"
    default     1
    choices
        "Yes" "--memory-efficient"
        "No" ""

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     "quast_results"

var "OUTPUT"
    type        chooser
    label       "Notify of completion by email"
    default     1
    choices
        "Send output by email" "bl_email.py --recipient %ADDRESS% --subject 'quast completed' --message quast.log;"
        "Show output on screen" "($BL_TextEditor quast.log)& ($BL_Browser report.html)& ($BL_Spreadsheet transposed_report.tsv)& (blreads)&"

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


panel
    var "Run"
        type        button
        label       "Run"
        shell       "echo 'Start: '`date` > quast.log; OUTDIR=`dirname %ASSEMBLY%`/%OUTNAME%; quast.sh  %REFERENCE% %EUKARYOTE% %SCAFFOLDS% %MEMORYEFFICIENT% --threads %THREADS% -o $OUTDIR %ASSEMBLY%  >> quast.log; RCODE=$?; echo 'Finish: '`date` >> quast.log; if [ $RCODE -eq '0' ]; then (mv quast.log $OUTDIR; cd $OUTDIR; %OUTPUT%) fi"
        close       true

    var "Help"
        type        button
        label       "Help"
        shell       "$BIRCH/script/chooseviewer.py $BIRCH/doc/pkg/quast/manual.html"
        close       false