Mercurial > repos > stevecassidy > vowelplot
changeset 3:24f05f509f09 draft
planemo upload commit e4adec77d8b4e6385b7db85ebbe01cfb85ed8de2
| author | stevecassidy |
|---|---|
| date | Fri, 14 Oct 2016 15:07:25 -0400 |
| parents | 3e7b945648a4 |
| children | 0c6aea9fe490 |
| files | phonR_tool.R phonR_tool.xml |
| diffstat | 2 files changed, 11 insertions(+), 29 deletions(-) [+] |
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--- 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('<html><body>', - '<h3>Result:</h3><img src="pngfile.png"/>', - '</html></body>'); -writeLines(html_output, htmlfile_handle); -close(htmlfile_handle);
--- 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 @@ </requirements> <command interpreter="Rscript"> - $__tool_directory__/phonR_tool.R --input="${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}" </command> <inputs> @@ -37,7 +37,7 @@ </inputs> <outputs> - <data format="html" name="htmlfile" label="output.html" /> + <data format="pdf" name="pdffile" label="vowelplot.pdf" /> </outputs> @@ -46,12 +46,8 @@ <param name="input" value="femaletest.tsv"/> <param name="f1" value='4' /> <param name="f2" value='5' /> - <param name="vowel" value="vowel"/> - <output name="output"> - <assert_contents> - <has_text text="html"/> - </assert_contents> - </output> + <param name="vowel" value='3'/> + <output name="output" file="femalevowelplot.pdf" compare="sim_size" /> </test> </tests>