# HG changeset patch
# User stevecassidy
# Date 1476472045 14400
# Node ID 24f05f509f0986eabba0d0b986cae9118fef0cad
# Parent 3e7b945648a404413b312341de11b8ac74b5bfee
planemo upload commit e4adec77d8b4e6385b7db85ebbe01cfb85ed8de2
diff -r 3e7b945648a4 -r 24f05f509f09 phonR_tool.R
--- a/phonR_tool.R Fri Oct 14 14:13:23 2016 -0400
+++ b/phonR_tool.R Fri Oct 14 15:07:25 2016 -0400
@@ -4,12 +4,11 @@
# Created by Michael Bauer
#
library(phonR)
-library('getopt')
+library(getopt)
#create options
option_specification = matrix(c(
- 'outdir', 'f', 1, 'character',
- 'htmlfile', 'h', 1, 'character',
+ 'pdffile', 'h', 1, 'character',
'inputfile', 'i', 1, 'character',
'column1', 'y', 1, 'integer',
'column2', 'z', 1, 'integer',
@@ -26,27 +25,14 @@
# Parse options
options = getopt(option_specification);
-if (!is.null(options$outdir)) {
- # Create the directory
- dir.create(options$outdir,FALSE)
-}
-
-pngfile <- gsub("[ ]+", "", paste(options$outdir,"/pngfile.png"))
-htmlfile <- gsub("[ ]+", "", paste(options$htmlfile))
+pdffile <- gsub("[ ]+", "", paste(options$pdffile))
data = read.table(options$inputfile,sep="\t", header=TRUE);
-png(pngfile);
+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,
+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();
-
-htmlfile_handle <- file(htmlfile)
-html_output = c('',
- 'Result:
',
- '');
-writeLines(html_output, htmlfile_handle);
-close(htmlfile_handle);
diff -r 3e7b945648a4 -r 24f05f509f09 phonR_tool.xml
--- a/phonR_tool.xml Fri Oct 14 14:13:23 2016 -0400
+++ b/phonR_tool.xml Fri Oct 14 15:07:25 2016 -0400
@@ -8,7 +8,7 @@
- $__tool_directory__/phonR_tool.R --input="${input}" --outdir="$htmlfile.files_path" --htmlfile="$htmlfile" --column1="${f1}" --column2="${f2}" --columnvowels="${vowel}" --pretty="${pretty}" --ellipse="${ellipse}" --tokens="${tokens}" --means="${means}" --cextokens="${cextokens}" --alphatokens="${alphatokens}" --cexmeans="${cexmeans}"
+ $__tool_directory__/phonR_tool.R --input="${input}" --pdffile="$pdffile" --column1="${f1}" --column2="${f2}" --columnvowels="${vowel}" --pretty="${pretty}" --ellipse="${ellipse}" --tokens="${tokens}" --means="${means}" --cextokens="${cextokens}" --alphatokens="${alphatokens}" --cexmeans="${cexmeans}"
@@ -37,7 +37,7 @@
-
+
@@ -46,12 +46,8 @@
-
-
+
+