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


public class Sample
public static void main(String[] args)
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++)
catch (Exception e)


<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>

<param name="sample_type" type="select" label="Choose type of sampling">
<option value="random">Random Sampling</option>
        <option value="whole">Whole Genome</option>
<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"/>

    <data format="txt" name="output" size="1x30" area="true"

  This tool helps plot the correlation function for the given input file


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