On Thu, Apr 25, 2013 at 5:37 PM, Ramon Tiburski
<ramao_tiago_tibur...@hotmail.com> wrote:
> Hi Peter,
> I have this:
> <command>filename $input $output</command>
> And my executable and xml are in the same directory
> Thank you

If you don't put the binary on the system $PATH, then you'll
need to give an explicit path to it. You could try something like
this in the short term while you are developing the tool:

<command>/mnt/galaxy/tools/my_stuff/filename $input $output</command>

If you intend to share this tool then you'll need to learn about
how automatic dependency installation works via a
tool_dependencies.xml file.

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