You are correct.  It's always passing even when it fails. There was nothing in 
the docs to indicate a pass. 

Sent from my iPhone

> On Apr 28, 2015, at 3:44 PM, John Chilton <jmchil...@gmail.com> wrote:
> 
> I feel like that stdio tag is going to cause it to always pass - even
> if the exit code is not 0. Am I wrong? I like:
> 
>  <stdio>
>      <exit_code range="1:" />
>  </stdio>
> 
> myself. Björn Grüning uses -
> 
> <stdio>
> <exit_code range="1:" />
> <exit_code range=":-1" />
> <regex match="Error:" />
> <regex match="Exception:" />
> </stdio>
> 
> which is a popular choice.
> 
> As a heads up for people reading discussion in the future - starting
> in 15.05 - you will be able to just add detect_errors="exit_code" on
> the command tag to get a more sensible default behavior.
> https://github.com/galaxyproject/galaxy/pull/117
> 
> -John
> 
> 
>> On Tue, Apr 28, 2015 at 12:12 PM, Ryan G <ngsbioinformat...@gmail.com> wrote:
>> <stdio>
>>  <exit_code range="-1" level="fatal" description="RandomSubFq failed" />
>> </stdio>
>> 
>> 
>> this works.  Thanks.
>> 
>> On Tue, Apr 28, 2015 at 11:51 AM, Dannon Baker <dannon.ba...@gmail.com>
>> wrote:
>>> 
>>> Like Peter mentions, we did this because historically not all tools used
>>> (still don't, I guess) exit codes correctly.  If yours does, you can set
>>> exit_code tags and everything should work.
>>> 
>>> On Tue, Apr 28, 2015 at 11:47 AM Ryan G <ngsbioinformat...@gmail.com>
>>> wrote:
>>>> 
>>>> 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.c...@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 <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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>>>> 
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>> 
>> 
>> 
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