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1 #' RScript capable
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2 #' Rscript plasmidprofile.R -b blast_runG.tsv -s srst2_runG.tsv -u 0.75 -l 10000 -t "This is a test" -a
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3
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4
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5 suppressPackageStartupMessages(library("optparse"))
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6 suppressPackageStartupMessages(library("Plasmidprofiler"))
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7 options(bitmapType='cairo')
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8
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9 cl_arguments <- function(){
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10 # CL arguments ####
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11 option_list = list(
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12 make_option(c("-b", "--blastfile"), type="character", default=NULL,
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13 help="BLAST TSV file name", metavar="character"),
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14 make_option(c("-s", "--srst2file"), type="character", default=NULL,
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15 help="SRST2 TSV file name", metavar="character"),
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16 make_option(c("-u", "--sureness"), type="numeric", default=NA,
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17 help="Sureness cut off [default = %default]", metavar="numeric"),
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18 make_option(c("-c", "--coverage"), type="numeric", default=NA,
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19 help="Percent coverage cut off", metavar="numeric"),
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20 make_option(c("-l", "--length"), type="numeric", default=NA,
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21 help="Plasmid length cut off", metavar="numeric"),
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22 make_option(c("-a", "--anonymize"), action="store_true", default=NA,
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23 help="Anonymize plasmid and sample names"),
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24 make_option(c("-o", "--outfile"), type="character", default="P2Run_",
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25 help="Output filename prefix [default= %default]", metavar="character"),
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26 make_option(c("-t", "--title"), type="character", default="Plasmid Profiles",
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27 help="Title of image [default = %default]", metavar="character"),
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28 make_option(c("-C", "--combineincs"), action="store_true", default=NA,
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29 help="Combine very closely related incompatibility groups. eg. ")
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30 # make_option(c("-T", "--Test"), action="store_true", default=NA,
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31 # help="Test filecache")
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32
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33 );
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34
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35 opt_parser <- OptionParser(option_list=option_list);
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36 opt <- parse_args(opt_parser);
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37
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38 if (is.null(opt$blastfile) | is.null(opt$srst2file)){
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39 print_help(opt_parser)
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40 stop("SRST2 and BLAST files must be supplied.", call.=FALSE)
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41 }
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42 opt
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43 }
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44
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45
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46 opt <- cl_arguments()
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47
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48 filecache <<- new.env(parent = .GlobalEnv)
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49 assign("name", opt$outfile, envir = filecache)
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50 assign("mods", "Subsampling applied: ", envir = filecache)
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51
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52 main(blast.file = opt$blastfile,
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53 srst2.file = opt$srst2file,
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54 coverage.filter = opt$coverage,
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55 sureness.filter = opt$sureness,
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56 length.filter = opt$length,
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57 anonymize = opt$anonymize,
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58 combine.inc = opt$combineincs,
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59 main.title = opt$title)
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