Hey Ryan,

Yes, this is exactly why.  By default, galaxy expects that anything written
to stderr means that there was a failure, though you can change this by
using the error_code syntax (among other options) found here:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

-Dannon

On Tue, Apr 28, 2015 at 11:41 AM Ryan G <ngsbioinformat...@gmail.com> wrote:

>  Hi - I implemented a tool I us into Galaxy but when I run the tool view
> Galaxy, Galaxy thinks the tool failed.  I checked the output file the tools
> create, and it succeeded.
>
> How do I tell Galaxy that a tool it ran was successful?  Is it something
> in my XML file?  The tool is outputting some info to stderr.  Could this be
> why?
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