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.

You'll need to (a) add an output file to your tool configuration ( see http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Coutputs.3E_ta... ) 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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