--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_barplot.R	Tue Feb 23 05:17:12 2016 -0500
@@ -0,0 +1,57 @@
+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',
+  'col', 'c', 2, 'character',
+  'bottom_margin', 'b', 2, 'integer',
+  'left_margin', 'l', 2, 'integer',
+  'top_margin', 't', 2, 'integer',
+  'right_margin', 'r', 2, 'integer'
+), byrow=TRUE, ncol=4);
+
+options = getopt(option_specification);
+
+data = read.table(options$input_file, sep = '\t', h = T)
+
+data_column = 2
+if(!is.null(options$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$col
+
+plot_barplot <- function(){
+    par(las=2)
+    par(mar=margin)
+    barplot(data[, data_column], horiz = T, xlab = xlab, 
+        names.arg = data[, names_column], col = col, cex.names=0.7, 
+        cex.axis = 0.8)
+}
+
+if(!is.null(options$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()
+}
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_barplot.xml	Tue Feb 23 05:17:12 2016 -0500
@@ -0,0 +1,88 @@
+<tool id="plot_barplot" name="Plot barplot" version="0.1.0">
+    <description>with R</description>
+
+    <requirements>
+        <requirement type="package" version="3.2.1">R</requirement>
+        <requirement type="package" version="1.20.0">getopt</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+
+    <version_command></version_command>
+
+    <command><![CDATA[
+        Rscript $__tool_directory__/plot_barplot.R
+            --input_file $input_file
+
+            #if str($output_format)=="pdf"
+                --output_pdf_file $output_pdf_file
+            #else
+                --output_svg_file $output_svg_file
+            #end if
+
+
+            --data_column $column_with_data
+            --names_column $names_column
+            --xlab $xlab
+            --col $col
+            --bottom_margin $bottom_margin
+            --left_margin $left_margin
+            --top_margin $top_margin
+            --right_margin $right_margin
+    ]]></command>
+
+    <inputs>
+        <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="File in tabular format with tab-separated columns and header in first line (--input_file)"/>
+
+        <param name="output_format" label="Format for output image" type="select" help="">
+            <option value="pdf" selected="True">PDF</option>
+            <option value="svg">SVG</option>
+        </param>
+
+        <param name="column_with_data" type="data_column" data_ref="input_file" multiple="false" numerical="true" label="Column containing data?" help="(--data_column)" />
+
+        <param name="names_column" type="data_column" data_ref="input_file" multiple="false" numerical="false" label="Column containing data names?" help="(--names_column)" />
+
+        <param name="xlab" type="text" value="" label="Label for x axis" help="(--xlab)"/>
+
+        <param name="col" label="Bar color" type="text" value= "blue" help="R color (--col)"/>
+
+        <param name="bottom_margin" type="integer" value="5" label="Bottom margin" help="(--bottom_margin)"/>
+        <param name="left_margin" type="integer" value="19" label="Left margin" help="(--left_margin)"/>
+        <param name="top_margin" type="integer" value="1" label="Top margin" help="(--top_margin)"/>
+        <param name="right_margin" type="integer" value="1" label="Right margin" help="(--right_margin)"/>
+    </inputs>
+
+    <outputs>
+        <data name="output_pdf_file" format="pdf"
+            label="${tool.name} on ${on_string}: PDF barplot">
+            <filter>output_format=="pdf"</filter>
+        </data>
+        <data name="output_png_file" format="png"
+            label="${tool.name} on ${on_string}: PNG barplot">
+            <filter>output_format=="png"</filter>
+        </data>
+        <data name="output_svg_file" format="svg"
+            label="${tool.name} on ${on_string}: SVG barplot">
+            <filter>output_format=="svg"</filter>
+        </data>
+    </outputs>
+
+    <tests>
+    </tests>
+
+    <help><![CDATA[
+        **What it does**
+
+        This tool plot a barplot from a tabular file into different format files given different customizable parameters.
+
+        This tool relies on R's barplot function.
+
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Feb 23 05:17:12 2016 -0500
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.2.1">
+        <repository changeset_revision="9f31a291b305" name="package_r_3_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="getopt" version="1.20.0">
+        <repository changeset_revision="a0851e07e3ac" name="package_r_3_2_1_getopt_1_20_0" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>