# 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        "newSOAPdenovo2 - 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 "LIBS2-4"

        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 "LIBS5-7"

        var "L5"
            type        chooser
            label       "Use LIB5?  -----------------------------"
            default     1
            choices
                "Yes" "echo %L5PEL1%,%L5PER1%'|'%L5PEL2%,%L5PER2%'|'%L5PEL3%,%L5PER3%'|'%L5PEL4%,%L5PER4%'^'asm_flags=%L5-ASM%'|'avg_ins=%L5-AVGINS%'|'rank=%L5-RANK%'|'rd_len_cutoff=%L5-MAXREAD%'|'reverse_seq=%L5-revseq% >> %in1%.in;"
                "No" ""

        var "L5-rank"
            type        number
            label       "order for use in assembly (rank) "
            min         1
            max         4
            default     1 

        panel
            var "L5PEL1"
                type        file
                label       "Read pair 1 Left"
                default     ""

            var "L5PER1"
                type        file
                label       "Right"
                default     ""

        panel
            var "L5PEL2"
                type        file
                label       "Read pair 2 Left"
                default     ""

            var "L5PER2"
                type        file
                label       "Right"
                default     ""

        panel
            var "L5PEL3"
                type        file
                label       "Read pair 3 Left"
                default     ""

            var "L5PER3"
                type        file
                label       "Right"
                default     ""

        panel
            var "L5PEL4"
                type        file
                label       "Read pair 4 Left"
                default     ""

            var "L5PER4"
                type        file
                label       "Right"
                default     ""

        var "L5-avgins"
            type        number
            label       "Avg. insert size"
            min         200
            max         10000
            default     300 

        var "L5-maxread"
            type        number
            label       "Max. read length"
            min         50
            max         20000
            default     150 

        var "L5-asm"
            type        combobox
            label       "Use reads for "
            default     2
            choices
                "contigs only"    "1"
                "scaffolds only"  "2"
                "contigs and scaffolds"    "3"

        var "L5-revseq"
            type        chooser
            label       "shoulds reads be reversed? (reverse_seq) "
            default     1
            choices
                "Yes"    "1"
                "No"     "0"


        var "L6"
            type        chooser
            label       "Use LIB6?  -----------------------------"
            default     1
            choices
                "Yes" "echo %L6PEL1%,%L6PER1%'|'%L6PEL2%,%L6PER2%'|'%L6PEL3%,%L6PER3%'|'%L6PEL4%,%L6PER4%'^'asm_flags=%L6-ASM%'|'avg_ins=%L6-AVGINS%'|'rank=%L6-RANK%'|'rd_len_cutoff=%L6-MAXREAD%'|'reverse_seq=%L6-revseq% >> %in1%.in;"
                "No" ""

        var "L6-rank"
            type        number
            label       "order for use in assembly (rank) "
            min         1
            max         4
            default     1 

        panel
            var "L6PEL1"
                type        file
                label       "Read pair 1 Left"
                default     ""

            var "L6PER1"
                type        file
                label       "Right"
                default     ""

        panel
            var "L6PEL2"
                type        file
                label       "Read pair 2 Left"
                default     ""

            var "L6PER2"
                type        file
                label       "Right"
                default     ""

        panel
            var "L6PEL3"
                type        file
                label       "Read pair 3 Left"
                default     ""

            var "L6PER3"
                type        file
                label       "Right"
                default     ""

        panel
            var "L6PEL4"
                type        file
                label       "Read pair 4 Left"
                default     ""

            var "L6PER4"
                type        file
                label       "Right"
                default     ""

        var "L6-avgins"
            type        number
            label       "Avg. insert size"
            min         200
            max         10000
            default     300 

        var "L6-maxread"
            type        number
            label       "Max. read length"
            min         50
            max         20000
            default     150 

        var "L6-asm"
            type        combobox
            label       "Use reads for "
            default     2
            choices
                "contigs only"    "1"
                "scaffolds only"  "2"
                "contigs and scaffolds"    "3"

        var "L6-revseq"
            type        chooser
            label       "shoulds reads be reversed? (reverse_seq) "
            default     1
            choices
                "Yes"    "1"
                "No"     "0"



        var "L7"
            type        chooser
            label       "Use LIB7?  -----------------------------"
            default     1
            choices
                "Yes" "echo %L7PEL1%,%L7PER1%'|'%L7PEL2%,%L7PER2%'|'%L7PEL3%,%L7PER3%'|'%L7PEL4%,%L7PER4%'^'asm_flags=%L7-ASM%'|'avg_ins=%L7-AVGINS%'|'rank=%L7-RANK%'|'rd_len_cutoff=%L7-MAXREAD%'|'reverse_seq=%L7-revseq% >> %in1%.in;"
                "No" ""

        var "L7-rank"
            type        number
            label       "order for use in assembly (rank) "
            min         1
            max         4
            default     1 

        panel
            var "L7PEL1"
                type        file
                label       "Read pair 1 Left"
                default     ""

            var "L7PER1"
                type        file
                label       "Right"
                default     ""

        panel
            var "L7PEL2"
                type        file
                label       "Read pair 2 Left"
                default     ""

            var "L7PER2"
                type        file
                label       "Right"
                default     ""

        panel
            var "L7PEL3"
                type        file
                label       "Read pair 3 Left"
                default     ""

            var "L7PER3"
                type        file
                label       "Right"
                default     ""

        panel
            var "L7PEL4"
                type        file
                label       "Read pair 4 Left"
                default     ""

            var "L7PER4"
                type        file
                label       "Right"
                default     ""

        var "L7-avgins"
            type        number
            label       "Avg. insert size"
            min         200
            max         10000
            default     300 

        var "L7-maxread"
            type        number
            label       "Max. read length"
            min         50
            max         20000
            default     150 

        var "L7-asm"
            type        combobox
            label       "Use reads for "
            default     2
            choices
                "contigs only"    "1"
                "scaffolds only"  "2"
                "contigs and scaffolds"    "3"

        var "L7-revseq"
            type        chooser
            label       "shoulds reads be reversed? (reverse_seq) "
            default     1
            choices
                "Yes"    "1"
                "No"     "0"


    # - - - - - - - - - - - - - - - - - - - - - - - 
    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 "
        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