[galaxy-dev] formatting output from a java tool

14 Jun 2013

      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.

[galaxy-dev] formatting output from a java tool

vijayalakshmi