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#
# Galaxy tool that plots Vowels using the phonR package.
# Accepts 8 inputs of the form <tsv data file> <output file name> <column1> <column2> <optPretty> <optEllipse> <optTokens> <optMeans>
# Created by Michael Bauer
#
library(phonR)
library(getopt)

#create options
option_specification = matrix(c(
  'pdffile', 'h', 1, 'character',
  'inputfile', 'i', 1, 'character',
  'column1', 'y', 1, 'integer',
  'column2', 'z', 1, 'integer',
  'columnvowels', 'x', 1, 'integer',
  'pretty', 'p', 1, 'logical',
  'ellipse', 'e', 1, 'logical',
  'tokens', 't', 1, 'logical',
  'means', 'm', 1, 'logical',
  'cextokens', 'c', 1, 'numeric',
  'alphatokens', 'a', 1, 'numeric',
  'cexmeans', 'b', 1, 'numeric'
), byrow=TRUE, ncol=4);

# Parse options
options = getopt(option_specification);

pdffile <- gsub("[ ]+", "", paste(options$pdffile))

data = read.table(options$inputfile,sep="\t", header=TRUE);

pdf(pdffile);

plotVowels(data[,options$column1], data[,options$column2], data[,options$columnvowels], plot.tokens = options$tokens,
          pch.tokens = data[,options$columnvowels], cex.tokens = options$cextokens, alpha.tokens = options$alphatokens,
          plot.means = options$means, pch.means = data[,options$columnvowels], cex.means = options$cexmeans,
          var.col.by = data[,options$columnvowels], ellipse.line = options$ellipse, pretty = options$pretty)
dev.off();