ok, thanks.  Let me look at this.  When I look at the information about the tool, Galaxy does see the exit code is 0, which I think would be sufficient to know the tool ran correctly.

On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

You probably need to set the <stdio> tag, since due to a
historical design choice by default any output on stderr
is treated as an error. See:

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax

Peter

On Tue, Apr 28, 2015 at 4:41 PM, Ryan G <ngsbioinformatics@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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