--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/karyotype/karyotype_plot.xml	Thu Jan 22 10:40:48 2015 -0500
@@ -0,0 +1,178 @@
+<tool id="karyotype_Plot_1" name="Karyotype Plotting tool" version="1.0.0">
+  <description>for multiple series </description>
+  <command interpreter="bash">\$R_SCRIPT_PATH/r_wrapper.sh $script_file</command>
+
+  <inputs>
+    <param name="main" type="text" value="" size="30" label="Plot Title"/>
+    <param name="xlab" type="text" value="" size="30" label="Label for x axis"/>
+    <param name="ylab" type="text" value="" size="30" label="Label for y axis"/>
+    <param name="lty" type="select" label="Backbone Line Type">
+	    <option value="1">Solid</option>
+	    <option value="2">Dashed</option>
+	    <option value="3">Dotted</option>
+	</param>
+	<param name="col" type="select" label="Backbone Line Color">
+	    <option value="1">Black</option>
+	    <option value="2">Red</option>
+	    <option value="3">Green</option>
+	    <option value="4">Blue</option>
+	    <option value="5">Cyan</option>
+	    <option value="6">Magenta</option>
+	    <option value="7">Yellow</option>
+	    <option value="8">Gray</option>
+	</param>
+	<param name="lwd" type="float" label="Backbone Line Width" value="1.0"/>
+	
+	<conditional name="legend">
+        <param name="status" type="select" label="Include legend?">
+          <option value="yes" selected="true">Yes</option>
+          <option value="no">No</option>
+        </param>
+	<when value="yes">
+		<param name="leg_title" type="text" value="" size="30" label="Legend title"/>
+		<param name="leg_pos" type="select" label="Legend position">
+          <option value="top" selected="true">top</option>
+          <option value="topright">topright</option>
+          <option value="topleft">topleft</option>
+          <option value="bottom">bottom</option>
+          <option value="bottomright">bottomright</option>
+          <option value="bottomleft">bottomleft</option>
+          <option value="left">left</option>
+          <option value="right">right</option>
+          <option value="center">center</option>
+        </param>	
+	</when>
+	<when value="no">
+    </when>
+    </conditional>
+    
+    <repeat name="series" title="Series">
+      <param name="input" type="data" format="tabular" label="Dataset"/>
+      <param name="chrcolumn" type="data_column" data_ref="input" label="Chromosome Column"/>
+      <param name="startcolumn" type="data_column" data_ref="input" numerical="True" label="Start Column"/>
+      <param name="endcolumn" type="data_column" data_ref="input" numerical="True" label="End Column"/>
+      <param name="fpch" type="select" label="Point Type">
+        <option value="1">Circle (hollow)</option>
+        <option value="2">Triangle (hollow)</option>
+        <option value="3">Cross</option>
+        <option value="4">Diamond (hollow)</option>
+        <option value="15">Square (filled)</option>
+        <option value="16">Circle (filled)</option>
+        <option value="17">Triangle (filled)</option>  
+      </param>
+      <param name="fcol" type="select" label="Point Color">
+        <option value="1">Black</option>
+        <option value="2">Red</option>
+        <option value="3">Green</option>
+        <option value="4">Blue</option>
+        <option value="5">Cyan</option>
+        <option value="6">Magenta</option>
+        <option value="7">Yellow</option>
+        <option value="8">Gray</option>
+      </param>
+      <param name="fcex" type="float" label="Point Scale" value="1.0"/>
+      <param name="leg_text" type="text" value="" size="30" label="Legend text" help="Will be printed only if Include Legend option is set to Yes"/>
+    </repeat>       
+  </inputs>
+
+  <configfiles>
+    <configfile name="script_file">
+      ## Setup R error handling to go to stderr
+      options( show.error.messages=F, 
+               error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) }, 
+               warn = -1 )
+      ## Determine range of all series in the plot
+      library('gtools')
+      chrlist = c()
+      coordrange = c( NULL, NULL )
+      #for $i, $s in enumerate( $series )
+        s${i} = read.table( "${s.input.file_name}" )
+        chrlist = union( chrlist, as.character(unique(s${i}[,${s.chrcolumn}])) )
+        coordrange = range( coordrange, range(s${i}[,${s.startcolumn}]), range(s${i}[,${s.endcolumn}])  )
+      #end for
+      chrlist=mixedsort(chrlist)
+      coordrange_byChr=list()
+      length(coordrange_byChr) = length(chrlist)*2
+      dim(coordrange_byChr) = c(length(chrlist),2)
+      ci=1
+      for (chr in chrlist) {
+	      #for $i, $s in enumerate( $series )
+	        s${i} = read.table( "${s.input.file_name}" )
+	        if (nrow(s${i}[s${i}[,${s.chrcolumn}]==chr,]) > 0) {
+	        coordrange_byChr[ci,]=range(coordrange_byChr[ci,], s${i}[s${i}[,${s.chrcolumn}]==chr,c(${s.startcolumn},${s.endcolumn})])
+	        }
+	      #end for
+	  ci=ci+1
+	  }
+      ## Open output PDF file
+      pdf( "${out_file1}" )
+      ## Dummy plot for axis / labels
+      plot( NULL, type="n", xlim=c(1,length(chrlist)), ylim=coordrange, axes=F, main="${main}", xlab="${xlab}", ylab="${ylab}" )
+      box()
+	  axis(1,at=1:length(chrlist),labels=chrlist,cex.axis=0.9, las=2)
+	  axis(2,at=seq(coordrange[1],coordrange[2], length.out=10))
+	  ## Plot backbone lines for each chr
+	  ci=1
+	  for (chr in chrlist) {
+	    lines(c(ci,ci),coordrange_byChr[ci,],lty=${lty},col=${col},lwd=${lwd})
+	    ci=ci+1
+	  }
+	  
+	  legend_text=c()
+	  pchlist=c()
+	  colorlist=c() 
+      ## Plot each series
+      #for $i, $s in enumerate( $series )
+      	chrs=as.character(s${i}[,${s.chrcolumn}])
+      	xvals=sapply(chrs,function(x) which(chrlist==x))
+      	points(xvals, s${i}[,${s.startcolumn}], pch=${s.fpch}, cex=${s.fcex}, col=${s.fcol} )
+      	legend_text[${i}+1] = "${s.leg_text}"
+      	pchlist[${i}+1] = ${s.fpch}
+      	colorlist[${i}+1] = ${s.fcol}
+      #end for
+      
+      #if $legend['status'] == "yes"
+	  legend_title = "$legend.leg_title"
+	  legend_pos = "$legend.leg_pos"
+	  legend(legend_pos, title=legend_title, legend=legend_text, pch=pchlist, col=colorlist)
+	  #end if
+	            
+      ## Close the PDF file
+      devname = dev.off() 
+    </configfile>
+  </configfiles>
+
+  <outputs>
+    <data format="pdf" name="out_file1" />
+  </outputs>
+  
+  <requirements>
+    	<requirement type="set_environment">R_SCRIPT_PATH</requirement>
+    	<requirement type="package" version="2.15.0">R</requirement>
+  </requirements>
+	
+<help>
+.. class:: infomark
+
+**What it does**
+
+This tool allows you to paint genomic regions of interest on chromosomes arranged in a karyotype-like fashion. It also allows you to have multiple series in a plot, with each series corresponding to a different feature/dataset.
+
+-----
+
+.. class:: warningmark
+
+Chromosome lengths (backbone line) are determined based on min and max co-ordinates (by chromosome) in start and end columns respectively. For the series, only the co-ordiantes in start column are used for plotting.
+
+-----
+
+**Example**
+
+Below is an example of a two series karyotype plot:
+
+.. image:: ./static/operation_icons/karyotype_output.png
+   :height: 540 
+   :width: 540
+
+</help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/karyotype/r_wrapper.sh	Thu Jan 22 10:40:48 2015 -0500
@@ -0,0 +1,23 @@
+#!/bin/sh
+
+### Run R providing the R script in $1 as standard input and passing 
+### the remaining arguments on the command line
+
+# Function that writes a message to stderr and exits
+function fail
+{
+    echo "$@" >&2
+    exit 1
+}
+
+# Ensure R executable is found
+which R > /dev/null || fail "'R' is required by this tool but was not found on path" 
+
+# Extract first argument
+infile=$1; shift
+
+# Ensure the file exists
+test -f $infile || fail "R input file '$infile' does not exist"
+
+# Invoke R passing file named by first argument to stdin
+R --vanilla --slave $* < $infile

Binary file karyotype/static/operation_icons/karyotype_output.png has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/karyotype/tool_dependencies.xml	Thu Jan 22 10:40:48 2015 -0500
@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <set_environment version="1.0">
+        <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+    <package name="R" version="2.15.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://CRAN.R-project.org/src/base/R-2/R-2.15.0.tar.gz</action>
+                <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
+                <action type="shell_command">make</action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R.
+        </readme>
+    </package>
+</tool_dependency>