name   "ABySS - de-novo genome assembly"
icon   "$BIRCH/dat/blreads/gsc-logo.png"
tip    "assemble a set of DNA reads into a genome, with no reference genome"

#-----------------------
# This menu does not implement the pe parameter of abyss-pe. An attempt was made
# to do that in abyss.blmenu.with-pe. However, when there are two tabs in a tabset,
# both having internal panels, the variables in the first tab fail to get substituted
# on the shell line. This is not explicitly forbidden in the formal PCD definition,
# but may not be fully implemented in BioLegato.
#  
# In summary, BioLegato seems to be able to handle one tab having panels, but not
# more than one may have panels.
#-----------------------

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

tabset

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

        var "jobname"
            type        text
            label       "Name for assembly"
            default     "abyss"   

        var "klength"
            type        number
            label       "k-mer length"
            min         32
            max         96
            default     64
 
        var "threads"
             type        number
             label       "Number of threads to use"
             min         1
             max         $BL_CORES_MAX
             default     $BL_CORES_DEFAULT

        var "ADDITIONAL"
            type        text
            label       "Additional abyss-pe parameters (eg. p=0.95)"
            default     ""        

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

        var "email"
            type        chooser
            label       "Notify of completion by email"
            default     1
            choices
                "Yes"    "bl_email.py --recipient %ADDRESS% --subject 'ABySS completed' --message abyss.log;"
                "No"     ""

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


    # - - - - - - - - - - - - - - - - - - - - - - - 
    tab "mate-pair reads"

        panel
            var "MPL1"
                type        file
                label       "Mate-pair 1 Left"

            var "MPR1"
                type        file
                label       "Right"
        panel
            var "MPL2"
                type        file
                label       "Mate-pair 2 Left"

            var "MPR2"
                type        file
                label       "Right"
        panel
            var "MPL3"
                type        file
                label       "Mate-pair 3 Left"

            var "MPR3"
                type        file
                label       "Right"
        panel
            var "MPL4"
                type        file
                label       "Mate-pair 4 Left"

            var "MPR4"
                type        file
                label       "Right"
        panel
            var "MPL5"
                type        file
                label       "Mate-pair 5 Left"

            var "MPR5"
                type        file
                label       "Right"
        panel
            var "MPL6"
                type        file
                label       "Mate-pair 6 Left"

            var "MPR6"
                type        file
                label       "Right"


    # - - - - - - - - - - - - - - - - - - - - - - - 
    tab "long reads"

        var "long1"
            type        file
            label       "long read file 1"

        var "long2"
            type        file
            label       "long read file 2"


        var "long3"
            type        file
            label       "long read file 3"


        var "long4"
            type        file
            label       "long read file 4"


        var "long5"
            type        file
            label       "long read file 5"


        var "long6"
            type        file
            label       "long read file 6"

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

        var "SE1"
            type        file
            label       "SE read file 1"

        var "SE2"
            type        file
            label       "SE read file 2"


        var "SE3"
            type        file
            label       "SE read file 3"


        var "SE4"
            type        file
            label       "SE read file 4"


        var "SE5"
            type        file
            label       "SE read file 5"


        var "SE6"
            type        file
            label       "SE read file 6"


panel
    # abyss-pe is a makefile. For whatever reasons, it simply will not allow command line substitution
    # of quoted lists eg. lib1='seqL.fq seqR.fq'. make seems to swallow the quotes, leaving things unquoted,
    # whenever quoted strings are passed to a script. The script itself must have the quotes.
    #   I've tried all permutations I can think of to get
    # parameters to substitute into the abyss-pe command line, but it doesn't process the lists as the man page
    # implies. The hack is to create a bash script that hard wires in the file paths with quotes, and then
    # run the bash script. I wasted a full day on this! Sheeeesh!!

    var "Run"
        type        button
        label       "Run"
#        shell       "echo %JOBNAME% %MPL1% %MPR1% %SE1% %SE2%  %LONG1% %LONG2%"
#        shell       "echo %MPL1%,%MPR1%'|'%MPL2%,%MPR2%'|'%MPL3%,%MPR3%'|'%MPL4%,%MPR4%'|'%MPL5%,%MPR5%'|'%MPL6%,%MPR6% > %in1%.mpfiles; echo %long1%'|'%long2%'|'%long3%'|'%long4%'|'%long5%'|'%long6% > %in1%.longfiles; echo %SE1%'|'%SE2%'|'%SE3%'|'%SE4%'|'%SE5%'|'%SE6% > %in1%.sefiles; (if test ! -e %OUTDIR% ; then (mkdir %OUTDIR%) fi); nice abyss-pe `bl_seqreadlist.py --tsv %in1% --mp %in1%.mpfiles --long %in1%.longfiles --s %in1%.sefiles --outtype abysscom`  name=%JOBNAME% -j %THREADS% -o %OUTDIR% ; cd %OUTDIR%; %EMAIL% blreads "
        shell       "echo %MPL1%,%MPR1%'|'%MPL2%,%MPR2%'|'%MPL3%,%MPR3%'|'%MPL4%,%MPR4%'|'%MPL5%,%MPR5%'|'%MPL6%,%MPR6% > %in1%.mpfiles; echo %long1%'|'%long2%'|'%long3%'|'%long4%'|'%long5%'|'%long6% > %in1%.longfiles; echo %SE1%'|'%SE2%'|'%SE3%'|'%SE4%'|'%SE5%'|'%SE6% > %in1%.sefiles; if test ! -e %OUTDIR% ; then (mkdir %OUTDIR%) fi; echo '#!/bin/bash' > %JOBNAME%.sh; echo abyss-pe  j=%THREADS% name=%JOBNAME% k=%KLENGTH% %ADDITIONAL% `bl_seqreadlist.py --tsv %in1% --mp %in1%.mpfiles --long %in1%.longfiles --s %in1%.sefiles --outtype abysscom --fullpaths` >> %JOBNAME%.sh; chmod u+x %JOBNAME%.sh; mv %JOBNAME%.sh %OUTDIR%; rm %in1%.*; cd %OUTDIR%; ./%JOBNAME%.sh 2>abyss.log; %EMAIL% blreads "

        close       true

    var "Manual"
        type        button
        label       "Manual"
        shell       "chooseviewer.py http://manpages.ubuntu.com/manpages/bionic/en/man1/abyss-pe.1.html"
        close       false