--- a/kaks_analysis_barplot.R	Wed Mar 08 09:08:50 2017 -0500
+++ b/kaks_analysis_barplot.R	Wed Mar 08 13:57:03 2017 -0500
@@ -3,8 +3,9 @@
 suppressPackageStartupMessages(library("optparse"))
 
 option_list <- list(
-    make_option(c("-c", "--components", action="store", dest="components", help="Ks significant components input dataset"),
-    make_option(c("-o", "--output", action="store", dest="output", default=NULL, help="Output dataset"),
+    make_option(c("-c", "--components_input"), action="store", dest="components_input", help="Ks significant components input dataset"),
+    make_option(c("-k", "--kaks_input"), action="store", dest="kaks_input", help="KaKs analysis input dataset"),
+    make_option(c("-o", "--output"), action="store", dest="output", help="Output dataset")
 )
 
 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
@@ -12,100 +13,103 @@
 opt <- args$options
 
 
-get_num_components=function(components_dataset)
+get_num_components = function(components_data)
 {
-    # Read in the components data.
-    components_data <- read.delim(components_dataset, header=TRUE);
     # Get the max of the number_comp column.
-    num_components <- max(components_data[3, ], na.rm=TRUE);
-    return = c(components_data, num_components)
-    return
+    number_comp = components_data[, 3]
+    num_components <- max(number_comp, na.rm=TRUE);
+    num_components
 }
 
-get_pi_mu_var = function(components_data, num_components) {
+get_pi_mu_var = function(components_data, num_components)
+{
     # FixMe: enhance this to generically handle any integer value for num_components.
-    if (num_components == 1) {
+    if (num_components == 1)
+    {
         pi <- c(components_data[1, 9]);
         mu <- c(components_data[1, 7]);
         var <- c(components_data[1, 8]);
-    } else if (num_components == 2) {
+    }
+    else if (num_components == 2)
+    {
         pi <- c(components_data[2, 9], components_data[3, 9]);
         mu <- c(components_data[2, 7], components_data[3, 7]);
         var <- c(components_data[2, 8], components_data[3, 8]);
-    } else if (num_components == 3) {
+    }
+    else if (num_components == 3)
+    {
         pi <- c(components_data[4, 9], components_data[5, 9], components_data[6, 9]);
         mu <- c(components_data[4, 7], components_data[5, 7], components_data[6, 7]);
         var <- c(components_data[4, 8], components_data[5, 8], components_data[6, 8]);
-    } else if (num_components == 4) {
+    }
+    else if (num_components == 4)
+    {
         pi <- c(components_data[7, 9], components_data[8, 9], components_data[9, 9], components_data[10, 9]);
         mu <- c(components_data[7, 7], components_data[8, 7], components_data[9, 7], components_data[10, 7]);
         var <- c(components_data[7, 8], components_data[8, 8], components_data[9, 8], components_data[10, 8]);
+    }
     return = c(pi, mu, var)
     return
 }
 
-plot_ks<-function(ksfile, pi, mu, var) {
-	#change bin width
-	bin <- 0.05 * seq(0, 40);
-	kaks <- read.table(file=ksfile, header=T);
-	kaks <- kaks[kaks$Ks<2,];
-	h.kst <- hist(kaks$Ks, breaks=bin, plot=F);
-	nc <- h.kst$counts;
-	vx <- h.kst$mids;
-	ntot <- sum(nc);
-	# Set margin for plot bottom, left top, right.
-	par(mai=c(0.5, 0.5, 0, 0));
-	# Plot dimension in inches.
-	par(pin=c(2.5, 2.5));
-	g <- calculate_fitted_density(pi, mu, var);
-	h <- ntot * 2.5 / sum(g);
-	vx <- seq(1, 100) * 0.02;
-	ymax <- max(nc) + 5;
-	barplot(nc, space=0.25, offset=0, width=0.04, xlim=c(0,2), ylim=c(0, ymax));
-	# Add x-axis.
-	axis(1);
-	color <- c('green', 'blue', 'black', 'red');
-	for (i in 1:length(mu)) {
-	   lines(vx, g[,i] * h, lwd=2, col=color[i]);
-	}
+plot_ks<-function(kaks_input, output, pi, mu, var)
+{
+    # Start PDF device driver to save charts to output.
+    pdf(file=output, bg="white")
+    # Change bin width
+    bin <- 0.05 * seq(0, 40);
+    kaks <- read.table(file=kaks_input, header=T);
+    kaks <- kaks[kaks$Ks<2,];
+    h.kst <- hist(kaks$Ks, breaks=bin, plot=F);
+    nc <- h.kst$counts;
+    vx <- h.kst$mids;
+    ntot <- sum(nc);
+    # Set margin for plot bottom, left top, right.
+    par(mai=c(0.5, 0.5, 0, 0));
+    # Plot dimension in inches.
+    par(pin=c(2.5, 2.5));
+    g <- calculate_fitted_density(pi, mu, var);
+    h <- ntot * 2.5 / sum(g);
+    vx <- seq(1, 100) * 0.02;
+    ymax <- max(nc) + 5;
+    barplot(nc, space=0.25, offset=0, width=0.04, xlim=c(0,2), ylim=c(0, ymax));
+    # Add x-axis.
+    axis(1);
+    color <- c('green', 'blue', 'black', 'red');
+    for (i in 1:length(mu))
+    {
+       lines(vx, g[,i] * h, lwd=2, col=color[i]);
+    }
 };
 
-calculate_fitted_density <- function(pi, mu, var) {
-	comp <- length(pi);
-	var <- var/mu^2;
-	mu <- log(mu);;
-	#calculate lognormal density
-	vx <- seq(1, 100) * 0.02;
-	fx <- matrix(0, 100, comp);
-	for (i in 1:100) {
-	    for (j in 1:comp) {
-	       fx[i, j] <- pi[j] * dlnorm(vx[i], meanlog=mu[j], sdlog=(sqrt(var[j])));
-	    };
-	 };
-	fx;
+calculate_fitted_density <- function(pi, mu, var)
+{
+    comp <- length(pi);
+    var <- var/mu^2;
+    mu <- log(mu);
+    #calculate lognormal density
+    vx <- seq(1, 100) * 0.02;
+    fx <- matrix(0, 100, comp);
+    for (i in 1:100)
+    {
+        for (j in 1:comp)
+        {
+           fx[i, j] <- pi[j] * dlnorm(vx[i], meanlog=mu[j], sdlog=(sqrt(var[j])));
+        };
+     };
+    fx;
 }
 
-# Read in the components data and get the number of components.
-items <- get_num_components(opt$components)
-components_data <- items[1]
-num_components <- items[2]
-
-# Set output file name.
-if (is.null(opt$output)) {
-    # Name the output file based on the name of the
-    # input file, properly handling full path if passed.
-    input_filename = basename(opt$components)
-    items = strsplit(input_filename, ".")
-    output_filename <- paste(items[1], ".components.", num_components, ".pdf")
-} else {
-    output_filename <- opt$output
-}
+# Read in the components data.
+components_data <- read.delim(opt$components_input, header=TRUE);
+# Get the number of components.
+num_components <- get_num_components(components_data)
 
 # Set pi, mu, var.
-items <- get_pi_mu_var(components_data, num_components)
-pi <- items[1]
-mu <- items[2]
-var <- items[3]
+items <- get_pi_mu_var(components_data, num_components);
+pi <- items[1];
+mu <- items[2];
+var <- items[3];
 
 # Plot the output.
-plot_ks(output_filename, pi, mu, var)
+plot_ks(opt$kaks_input, opt$output, pi, mu, var);

--- a/kaks_analysis_barplot.xml	Wed Mar 08 09:08:50 2017 -0500
+++ b/kaks_analysis_barplot.xml	Wed Mar 08 13:57:03 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="kaks_barplot" name="Orthologous or paralogous ks analyses barplot" version="1.0.0">
+<tool id="kaks_barplot" name="Orthologous or paralogous KaKs barplot" version="1.0.0">
     <description></description>
     <requirements>
          <requirement type="package" version="1.3.0">r-optparse</requirement>
@@ -6,12 +6,14 @@
     <command>
         <![CDATA[
             Rscript $__tool_directory__/kaks_analysis_barplot.R
-            -s '${components}'
+            -k '${kaks}'
+            -c '${components}'
             -o "$output"
         ]]>
     </command>
     <inputs>
-        <param name="components" format="tabular" type="data" label="Select dataset containing significant components in the ks distribution" />
+        <param name="kaks" format="tabular" type="data" label="KaKs analysis file" />
+        <param name="components" format="tabular" type="data" label="Significant components in the ks distribution" />
     </inputs>
     <outputs>
         <data name="output" format="pdf"/>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/components.tabular	Wed Mar 08 13:57:03 2017 -0500
@@ -0,0 +1,7 @@
+species	n	number_comp	lnL	AIC	BIC	mean	variance	porportion
+species1	1160	1	-1404.9900	2813.98	2824.09	0.4426	0.1293	1.00
+species1	1160	2	-1353.6550	2717.31	2742.59	0.7376	0.1672	0.61
+						0.2000	0.0069	0.39
+species1	1160	3	-1323.7480	2663.50	2703.94	0.1214	0.0002	0.10
+						0.7759	0.1663	0.57
+						0.2428	0.0070	0.33

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kaks.tabular	Wed Mar 08 13:57:03 2017 -0500
@@ -0,0 +1,1161 @@
+SEQ1	SEQ2	Ka	Ks	Ka\Ks
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