diff phonR_tool.R @ 0:3d068b7441be draft

planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
author stevecassidy
date Wed, 31 Aug 2016 22:06:23 -0400
parents
children 24f05f509f09
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phonR_tool.R	Wed Aug 31 22:06:23 2016 -0400
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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(
+  'outdir', 'f', 1, 'character',
+  'htmlfile', '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);
+
+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))
+
+data = read.table(options$inputfile,sep="\t", header=TRUE);
+
+png(pngfile);
+
+plotVowels(data[,options$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('<html><body>',
+                '<h3>Result:</h3><img src="pngfile.png"/>',
+                '</html></body>');
+writeLines(html_output, htmlfile_handle);
+close(htmlfile_handle);