--- a/ks_distribution.R	Thu Jun 08 10:32:44 2017 -0400
+++ b/ks_distribution.R	Fri Jun 23 14:12:59 2017 -0400
@@ -5,22 +5,15 @@
 option_list <- list(
     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")
+    make_option(c("-n", "--num_comp"), action="store", dest="num_comp", type="integer", help="Number of significant components in the Ks distribution"),
+    make_option(c("-o", "--output"), action="store", dest="output", help="Output dataset"),
+    make_option(c("-r", "--colors"), action="store", default=NA, help="List of component colors"),
 )
 
 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
 args <- parse_args(parser, positional_arguments=TRUE)
 opt <- args$options
 
-
-get_num_components = function(components_data)
-{
-    # Get the max of the number_comp column.
-    number_comp = components_data[, 3]
-    num_components <- max(number_comp, na.rm=TRUE)
-    return(num_components)
-}
-
 get_pi_mu_var = function(components_data, num_components)
 {
     # FixMe: enhance this to generically handle any integer value for num_components.
@@ -64,7 +57,7 @@
     return(results)
 }
 
-plot_ks<-function(kaks_input, output, pi, mu, var)
+plot_ks<-function(kaks_input, num_components, colors, output, pi, mu, var)
 {
     # Start PDF device driver to save charts to output.
     pdf(file=output, bg="white")
@@ -89,7 +82,51 @@
     barplot(nc, space=0.25, offset=0, width=0.04, xlim=c(0, max_ks), ylim=c(0, ymax), col="lightpink1", border="lightpink3")
     # Add x-axis.
     axis(1)
-    color <- c('red', 'yellow','green','black','blue', 'darkorange' )
+    if(is.na(colors)
+    {
+        color <- c('red', 'yellow', 'green', 'black', 'blue', 'darkorange')
+    }
+    else
+    {
+        # Handle specified colors for components.
+        cStr <- unlist(colors)
+        color <- c()
+        items <- strsplit(cStr, ",")
+        for (item in items) {
+            color <- c(color, item)
+        }
+        num_colors_specified = length(color)
+        if num_colors_specified < num_components:
+        {
+            for (i in num_colors_specified:num_components)
+            {
+                if !(any(color=='red')
+                {
+                    color <- c(color, 'red')
+                }
+                else if !(any(color=='yellow')
+                {
+                    color <- c(color, 'yellow')
+                }
+                else if !(any(color=='green')
+                {
+                    color <- c(color, 'green')
+                }
+                else if !(any(color=='black')
+                {
+                    color <- c(color, 'black')
+                }
+                else if !(any(color=='blue')
+                {
+                    color <- c(color, 'blue')
+                }
+                else
+                {
+                    color <- c(color, 'darkorange')
+                }
+            }
+        }
+    }
     for (i in 1:length(mu))
     {
        lines(vx, g[,i] * h, lwd=2, col=color[i])
@@ -117,8 +154,7 @@
 
 # Read in the components data.
 components_data <- read.delim(opt$components_input, header=TRUE)
-# Get the number of components.
-num_components <- get_num_components(components_data)
+num_components <- opt$num_comp
 
 # Set pi, mu, var.
 items <- get_pi_mu_var(components_data, num_components)
@@ -160,4 +196,4 @@
 }
 
 # Plot the output.
-plot_ks(opt$kaks_input, opt$output, pi, mu, var)
+plot_ks(opt$kaks_input, num_components, opt$colors, opt$output, pi, mu, var)

--- a/ks_distribution.xml	Thu Jun 08 10:32:44 2017 -0400
+++ b/ks_distribution.xml	Fri Jun 23 14:12:59 2017 -0400
@@ -1,18 +1,41 @@
-<tool id="ks_distribution" name="KsDistribution" version="1.0.0">
+<tool id="ks_distribution" name="KsDistribution" version="1.0.1">
     <description>plots the distribution of synonymous substitution (Ks) rates and fits significant component(s)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements_ks_distribution" />
     <command detect_errors="exit_code"><![CDATA[
+import json
 Rscript $__tool_directory__/ks_distribution.R
 -k '$input'
 -c '$components'
+-n $input.num_components
 -o '$output'
+#if str($choose_colors_cond.choose_colors) == 'yes':
+    #set ccs = list()
+    #for $i in $choose_colors_cond.colors:
+        $ccs.append($i.color)
+    #end for
+    -r '#echo json.dumps(ccs)#'
+#end if
     ]]></command>
     <inputs>
         <param name="input" format="tabular" type="data" label="KaKsAnalysis tabular file" />
-        <param name="components" format="tabular" type="data" label="Significant components" />
+        <param name="components" format="ptkscmp" type="data" label="Significant components" />
+        <conditional name="choose_colors_cond">
+            <param name="choose_colors" type="select" label="Choose colors for significant components">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <repeat name="colors" title="Component colors" min="1">
+                    <param name="color" type="select" label="Color">
+                        <expand macro="color_selector" />
+                    </param>
+                </repeat>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <data name="output" format="pdf"/>
@@ -20,7 +43,7 @@
     <tests>
         <test>
             <param name="input" value="kaks_input1.tabular" ftype="tabular" />
-            <param name="components" value="components.tabular" ftype="tabular" />
+            <param name="components" value="components.ptkscmp" ftype="ptkscmp" />
             <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
         </test>
     </tests>
@@ -37,6 +60,9 @@
 
  * **Synonymous substitution rates** - estimated synonymous substitution (Ks) rates output file produced by the KaKsAnalysis tool selected from your history.
  * **Synonymous components** - estimated significant component(s) output file produced by the KaKsAnalysis tool selected from your history.
+ * **Choose colors for significant components** - select 'Yes' to specify component colors or 'No' for colors chosen randlomly.
+
+   * **Component colors** - select a color from the palette for each component (colors will be chosen randomly for unspecified components).
     </help>
     <citations>
         <expand macro="citation1" />

--- a/macros.xml	Thu Jun 08 10:32:44 2017 -0400
+++ b/macros.xml	Fri Jun 23 14:12:59 2017 -0400
@@ -3,7 +3,7 @@
     <token name="@WRAPPER_VERSION@">1.0</token>
     <xml name="requirements_assembly_post_processor">
         <requirements>
-            <requirement type="package" version="1.0.0">plant_tribes_assembly_post_processor</requirement>
+            <requirement type="package" version="1.0.1">plant_tribes_assembly_post_processor</requirement>
         </requirements>
     </xml>
     <xml name="requirements_gene_family_aligner">
@@ -117,6 +117,14 @@
             </when>
         </conditional>
     </xml>
+    <xml name="color_selector">
+        <option value="255,0,0" selected="True">red</option>
+        <option value="0,255,0">green</option>
+        <option value="0,0,255">blue</option>
+        <option value="255,255,0">yellow</option>
+        <option value="255,140,0">dark orange</option>
+        <option value="0,0,0">black</option>
+    </xml>
     <xml name="citation1">
         <citation type="bibtex">
             @misc{None,