You'll need to (a) add an output file to your tool configuration ( see 
http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Coutputs.3E_tag_set
 ) and (b) write your output to the file. See other tool wrappers (e.g. 
/tools/filters/cutWrapper.xml) for an example.

Good luck,
J.

On Jun 14, 2013, at 1:07 PM, vijayalakshmi wrote:

> Hi,
> 
>    I am trying to integrate a tool that is written in java into galaxy. The 
> following is what I've done.
> 
> 1) Created a directory inside /tools directory and put my xml and runnable 
> jar file in it.
> 2) Linked the xml file in 'tool_conf.xml'.
> 
> tool_conf.xml
> 
>         <section name="sample tool" id="sample_tool">
>               <tool file="Sample/sample.xml"/>
>       </section>
> 
> sample.xml
> 
>         <tool id="sample" name="Compute correlation">
>                <command>java -jar sample.jar</command>
>         </tool>
> 
> sample.java (exported into a runnable jar file from eclipse)
> 
>          package Sample;
>          public class Sample 
>          {
>                public static void main(String[] args)
>                {
>                         System.out.println("Hello world this is important");
>                }
>          }
> 
> When I run the above, (i.e when I click on execute in the middle pane), 
> nothing gets added to my current history. Since there is no visual output of 
> any sort, I am not able to figure out where the problem lies. 
> 
> Any help or pointer is appreciated!
> Thanks y'all!
> VJ.
> 
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