annotate plot_barplot.R @ 1:7e3103db022d draft default tip

planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit 5653f2982dc5aeccd7701970fdfea444e3e53e3c-dirty

library('getopt')

option_specification = matrix(c(
  'input_file', 'i', 2, 'character',
  'output_pdf_file', 'p', 2, 'character',
  'output_png_file', 'o', 2, 'character',
  'output_svg_file', 's', 2, 'character',
  'data_column', 'd', 2, 'integer',
  'names_column', 'n', 2, 'integer',
  'xlab', 'x', 2, 'character',
  'log', 'g', 2, 'logical',
  'col', 'c', 2, 'character',
  'bottom_margin', 'b', 2, 'integer',
  'left_margin', 'l', 2, 'integer',
  'top_margin', 't', 2, 'integer',
  'right_margin', 'r', 2, 'integer',
  'header','y',2,'logical'
), byrow=TRUE, ncol=4);

options = getopt(option_specification);

header = TRUE
if(!is.null(options$header)) header = options$header

data = read.table(options$input_file, sep = '\t', h = header)

data_column = 2
if(!is.null(options$data_column)) data_column = options$data_column
names_column = 1
if(!is.null(options$names_column)) names_column = options$names_column

margin = c(5,19,1,1)
if(!is.null(options$bottom_margin)) margin[1] = options$bottom_margin
if(!is.null(options$left_margin)) margin[2] = options$left_margin
if(!is.null(options$top_margin)) margin[3] = options$top_margin
if(!is.null(options$right_margin)) margin[4] = options$right_margin

xlab = ""
if(!is.null(options$xlab)) xlab = options$xlab

col = "grey"
if(!is.null(options$col)) col = options$col

log = ""
if(!is.null(options$log) && options$log) log = "x"

plot_barplot <- function(){
    par(las=2)
    par(mar=margin)
    barplot(data[, data_column], horiz = T, xlab = xlab, 
        names.arg = data[, names_column], col = col, cex.names=0.7, 
        cex.axis = 0.8, log = log)
}

if(!is.null(options$output_pdf_file)){
    pdf(options$output_pdf_file)
    plot_barplot()
    dev.off()
}

if(!is.null(options$output_svg_file)){
    svg(options$output_svg_file)
    plot_barplot()
    dev.off()
}