Luqman, You can have multiple outputs. You simply list them individually under the outputs tag, such as in the following example: <outputs> <data format="sam" name="output1" /> <data format="fasta" name="output2" /> <data format="tabular" name="output3" /> </outputs> When passing the arguments in the command tag, you just refer to them as $output1, $output2, $output3, and so on. If you need to, you can also have variable numbers of outputs (based on different conditions in your XML). Let us know if you need information on how to do that, or on anything else. Regards, Kelly On Nov 5, 2009, at 5:02 AM, Luqman Hakim B Abdul Hadi wrote: