# This blmenu file is a workaround of a bug in BioLegato that limits
# recursive evaluation of variables when there are multiple panels within
# multiple tabs. The solution is to have one set of panels in the main tab,
# and all the rest of the panels in a second tab.
name        "SOAPdenovo2 - genome assembly"
tip    "denovo genome assembly"
system
    linux    amd64
       
var "in1"
    type        tempfile
    direction   in
    format      tsv
    save        false

tabset

    # - - - - - - - - - - - - - - - - - - - - - - - 
    tab    "Parameters"

        var "program"
            type        chooser
            label       "max. k-mer size"
            default     0
            choices
                "63" "SOAPdenovo-63mer"
                "127" "SOAPdenovo-127mer" 

        var "kmer"
            type        number
            label       "k-mer size (-K)"
            min         13
            max         127
            default     23

        var "genome"
            type        number
            label       "Genome size (Mb) (-N)"
            min         1
            max         100000
            default     20

        var "resolve"
            type        chooser
            label       "Use reads to resolve repeats?"
            default     1
            choices
                "Yes" "-R"
                "No" "" 

        var "mergelevel"
            type        number
            label       "strength of merging similar seqs. (-M)"
            min         0
            max         3
            default     1 

        var "mincontig"
            type        number
            label       "shortest contig for scaffolding (-L)"
            min         50
            max         200
            default     100

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

        var "additional"
            type        text
            label       "Additional SOAPdenovo2 parameters"
            default     ""  

        # - - - - - - - - - - - - - - - - - - - - - - - 

        var "L1"
            type        chooser
            label       "Use LIB1?  -----------------------------"
            default     0
            choices
                "Yes" "echo %L1PEL1%,%L1PER1%'|'%L1PEL2%,%L1PER2%'|'%L1PEL3%,%L1PER3%'|'%L1PEL4%,%L1PER4%'^'asm_flags=%L1-ASM%'|'avg_ins=%L1-AVGINS%'|'rank=%L1-RANK%'|'rd_len_cutoff=%L1-MAXREAD%'|'reverse_seq=%L1-revseq% > %in1%.in;"
                "No" ""

        var "L1-rank"
            type        number
            label       "order for use in assembly (rank) "
            min         1
            max         4
            default     1 

        panel
            var "L1PEL1"
                type        file
                label       "Read pair 1 Left"
                default     ""

            var "L1PER1"
                type        file
                label       "Right"
                default     ""

        panel
            var "L1PEL2"
                type        file
                label       "Read pair 2 Left"
                default     ""

            var "L1PER2"
                type        file
                label       "Right"
                default     ""

        panel
            var "L1PEL3"
                type        file
                label       "Read pair 3 Left"
                default     ""

            var "L1PER3"
                type        file
                label       "Right"
                default     ""

        panel
            var "L1PEL4"
                type        file
                label       "Read pair 4 Left"
                default     ""

            var "L1PER4"
                type        file
                label       "Right"
                default     ""

        var "L1-avgins"
            type        number
            label       "Avg. insert size"
            min         200
            max         10000
            default     300 

        var "L1-maxread"
            type        number
            label       "Max. read length"
            min         50
            max         20000
            default     150 

        var "L1-asm"
            type        combobox
            label       "Use reads for "
            default     2
            choices
                "contigs only"    "1"
                "scaffolds only"  "2"
                "contigs and scaffolds"    "3"

        var "L1-revseq"
            type        chooser
            label       "shoulds reads be reversed? (reverse_seq) "
            default     1
            choices
                "Yes"    "1"
                "No"     "0"


    # - - - - - - - - - - - - - - - - - - - - - - - 
    tab "additional PE"

        var "L2"
            type        chooser
            label       "Use LIB2?  -----------------------------"
            default     1
            choices
                "Yes" "echo %L2PEL1%,%L2PER1%'|'%L2PEL2%,%L2PER2%'|'%L2PEL3%,%L2PER3%'|'%L2PEL4%,%L2PER4%'^'asm_flags=%L2-ASM%'|'avg_ins=%L2-AVGINS%'|'rank=%L2-RANK%'|'rd_len_cutoff=%L2-MAXREAD%'|'reverse_seq=%L2-revseq% >> %in1%.in;"
                "No" ""

        var "L2-rank"
            type        number
            label       "order for use in assembly (rank) "
            min         1
            max         4
            default     1 

        panel
            var "L2PEL1"
                type        file
                label       "Read pair 1 Left"
                default     ""

            var "L2PER1"
                type        file
                label       "Right"
                default     ""

        panel
            var "L2PEL2"
                type        file
                label       "Read pair 2 Left"
                default     ""

            var "L2PER2"
                type        file
                label       "Right"
                default     ""

        panel
            var "L2PEL3"
                type        file
                label       "Read pair 3 Left"
                default     ""

            var "L2PER3"
                type        file
                label       "Right"
                default     ""

        panel
            var "L2PEL4"
                type        file
                label       "Read pair 4 Left"
                default     ""

            var "L2PER4"
                type        file
                label       "Right"
                default     ""

        var "L2-avgins"
            type        number
            label       "Avg. insert size"
            min         200
            max         10000
            default     300 

        var "L2-maxread"
            type        number
            label       "Max. read length"
            min         50
            max         20000
            default     150 

        var "L2-asm"
            type        combobox
            label       "Use reads for "
            default     2
            choices
                "contigs only"    "1"
                "scaffolds only"  "2"
                "contigs and scaffolds"    "3"

        var "L2-revseq"
            type        chooser
            label       "shoulds reads be reversed? (reverse_seq) "
            default     1
            choices
                "Yes"    "1"
                "No"     "0"



        var "L3"
            type        chooser
            label       "Use LIB3?  -----------------------------"
            default     1
            choices
                "Yes" "echo %L3PEL1%,%L3PER1%'|'%L3PEL2%,%L3PER2%'|'%L3PEL3%,%L3PER3%'|'%L3PEL4%,%L3PER4%'^'asm_flags=%L3-ASM%'|'avg_ins=%L3-AVGINS%'|'rank=%L3-RANK%'|'rd_len_cutoff=%L3-MAXREAD%'|'reverse_seq=%L3-revseq% >> %in1%.in;"
                "No" ""

        var "L3-rank"
            type        number
            label       "order for use in assembly (rank) "
            min         1
            max         4
            default     1 

        panel
            var "L3PEL1"
                type        file
                label       "Read pair 1 Left"
                default     ""

            var "L3PER1"
                type        file
                label       "Right"
                default     ""

        panel
            var "L3PEL2"
                type        file
                label       "Read pair 2 Left"
                default     ""

            var "L3PER2"
                type        file
                label       "Right"
                default     ""

        panel
            var "L3PEL3"
                type        file
                label       "Read pair 3 Left"
                default     ""

            var "L3PER3"
                type        file
                label       "Right"
                default     ""

        panel
            var "L3PEL4"
                type        file
                label       "Read pair 4 Left"
                default     ""

            var "L3PER4"
                type        file
                label       "Right"
                default     ""

        var "L3-avgins"
            type        number
            label       "Avg. insert size"
            min         200
            max         10000
            default     300 

        var "L3-maxread"
            type        number
            label       "Max. read length"
            min         50
            max         20000
            default     150 

        var "L3-asm"
            type        combobox
            label       "Use reads for "
            default     2
            choices
                "contigs only"    "1"
                "scaffolds only"  "2"
                "contigs and scaffolds"    "3"

        var "L3-revseq"
            type        chooser
            label       "shoulds reads be reversed? (reverse_seq) "
            default     1
            choices
                "Yes"    "1"
                "No"     "0"



        var "L4"
            type        chooser
            label       "Use LIB4?  -----------------------------"
            default     1
            choices
                "Yes" "echo %L4PEL1%,%L4PER1%'|'%L4PEL2%,%L4PER2%'|'%L4PEL3%,%L4PER3%'|'%L4PEL4%,%L4PER4%'^'asm_flags=%L4-ASM%'|'avg_ins=%L4-AVGINS%'|'rank=%L4-RANK%'|'rd_len_cutoff=%L4-MAXREAD%'|'reverse_seq=%L4-revseq% >> %in1%.in;"
                "No" ""

        var "L4-rank"
            type        number
            label       "order for use in assembly (rank) "
            min         1
            max         4
            default     1 

        panel
            var "L4PEL1"
                type        file
                label       "Read pair 1 Left"
                default     ""

            var "L4PER1"
                type        file
                label       "Right"
                default     ""

        panel
            var "L4PEL2"
                type        file
                label       "Read pair 2 Left"
                default     ""

            var "L4PER2"
                type        file
                label       "Right"
                default     ""

        panel
            var "L4PEL3"
                type        file
                label       "Read pair 3 Left"
                default     ""

            var "L4PER3"
                type        file
                label       "Right"
                default     ""

        panel
            var "L4PEL4"
                type        file
                label       "Read pair 4 Left"
                default     ""

            var "L4PER4"
                type        file
                label       "Right"
                default     ""

        var "L4-avgins"
            type        number
            label       "Avg. insert size"
            min         200
            max         10000
            default     300 

        var "L4-maxread"
            type        number
            label       "Max. read length"
            min         50
            max         20000
            default     150 

        var "L4-asm"
            type        combobox
            label       "Use reads for "
            default     2
            choices
                "contigs only"    "1"
                "scaffolds only"  "2"
                "contigs and scaffolds"    "3"

        var "L4-revseq"
            type        chooser
            label       "shoulds reads be reversed? (reverse_seq) "
            default     1
            choices
                "Yes"    "1"
                "No"     "0"

    # - - - - - - - - - - - - - - - - - - - - - - - 
    tab    "SE reads"

        var "LIBSE"
            type        chooser
            label       "Use LIBSE?  -----------------------------"
            default     1
            choices
                "Yes" "echo %SE1%'|'%SE2%'|'%SE3%'|'%SE4%'|'%SE5%'|'%SE6%'^'asm_flags=%L1-ASM%'|'rank=%L1-RANK% >> %in1%.in;"
                "No" ""

        var "L1-rank"
            type        number
            label       "order for use in assembly (rank) "
            min         1
            max         4
            default     1 

        var "SE1"
            type        file
            label       "SE Read 1"
            default     ""

        var "SE2"
            type        file
            label       "SE Read 2"
            default     ""

        var "SE3"
            type        file
            label       "SE Read 3"
            default     ""

        var "SE4"
            type        file
            label       "SE Read 4"
            default     ""

        var "SE5"
            type        file
            label       "SE Read 5"
            default     ""

        var "SE6"
            type        file
            label       "SE Read 6"
            default     ""

        var "SE-asm"
            type        combobox
            label       "Use reads for "
            default     2
            choices
                "contigs only"    "1"
                "scaffolds only"  "2"
                "contigs and scaffolds"    "3"

    # - - - - - - - - - - - - - - - - - - - - - - - 
    tab    "Output"

        var "outdir"
            type        text
            label       "Name for output directory"
            default     "../reads.trimmed.corrected.SOAPdenovo2"

        var "prefix"
            type        text
            label       "prefix for output filenames"
            default     "SOAPdenovo2"

        # Enclose %ADDRESS% in single quotes, which prevents
        # an error if no custom adaptor sequence is specified.
        var "email"
            type        chooser
            label       "Notify of completion by email"
            default     1
            choices
                "Yes" "bl_email.py --recipient %ADDRESS% --subject 'SOAPdenovo2 completed' --message soapdenovo2.log;"
                "No" "$BL_TextEditor soapdenovo2.log"

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

panel
    var "Run"
        type        button
        label       "Run"
        #shell       "echo %L1PEL1%,%L1PER1%'|'%L1PEL2%,%L1PER2%'|'%L1PEL3%,%L1PER3%'|'%L1PEL4%,%L1PER4%'^'asm_flags=%L1-ASM%'|'avg_ins=%L1-AVGINS%'|'rank=%L1-RANK%'|'rd_len_cutoff=%L1-MAXREAD%'|'reverse_seq=%L1-revseq% > %in1%.in; %L2% %L3% %L4% nice bl_soapdenovo2.py %in1%.in %OUTDIR% %PREFIX% %PROGRAM% %KMER% %GENOME% %RESOLVE% -M %MERGELEVEL% -L %MINCONTIG% -p %THREADS% %ADDITIONAL%; rm %in1%.in; cd %OUTDIR%; %EMAIL% blreads "
        shell       "%L1% %L2% %L3% %L4% %LIBSE% nice bl_soapdenovo2.py %in1%.in %OUTDIR% %PREFIX% %PROGRAM% %KMER% %GENOME% %RESOLVE% -M %MERGELEVEL% -L %MINCONTIG% -p %THREADS% %ADDITIONAL%; rm %in1%.in; cd %OUTDIR%; %EMAIL% blreads "

        close       true
    var "Hints"
        type        button
        label       "Hints"
        shell       "$BIRCH/script/chooseviewer.py $BIRCH/doc/bioLegato/blreads/SOAPdenovo2.hints.html"
        close       false

    var "Guide"
        type        button
        label       "Guide"
        shell       "chooseviewer.py http://github.com/aquaskyline/SOAPdenovo2/blob/master/README.md"
        close       false