Hi all, I am trying to integrate a tool written in java into galaxy. The tool opens a GUI window to output a graph and also writes a text file. I want to know how to output that graph in the middle pane and how to output the text file so that the user will be able to download it. *Sample.java* public class Sample { public static void main(String[] args) { try { int length = args.length; FileWriter fw = new FileWriter(args[length-1]+".txt"); fw.write("length = " + args.length); for(int i=0;i<args.length;i++) fw.write(args[i]); fw.close(); } catch (Exception e) { e.printStackTrace(); } } } *sample.xml* <tool id="sample" name="Compute correlation"> <description> for the given BAM file </description> <command>java -jar sample.jar $sample_type $window_frame_size $iteration $resolution $correlation_window_size $no_of_CPUs $output</command> <inputs> <param name="sample_type" type="select" label="Choose type of sampling"> <option value="random">Random Sampling</option> <option value="whole">Whole Genome</option> </param> <param name="window_frame_size" type="text" area="true" size="1x10" label="Frame size for extraction" help="Default:50000"/> <param name="iteration" type="text" area="true" size="1x10" label="Number of iterations per chromosome" help="Default:10"/> <param name="resolution" type="text" area="true" size="1x10" label="Resolution" help="Default:1"/> <param name="correlation_window_size" type="text" area="true" size="1x10" label="Correlation window Size" help="Default:1001"/> <param name="no_of_CPUs" type="text" area="true" size="1x5" label="Number of CPUs required" help="Default:1"/> </inputs> <outputs> <data format="txt" name="output" size="1x30" area="true" label="output"/> </outputs> <help> This tool helps plot the correlation function for the given input file </help> </tool> Thanks, VJ.