<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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>>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
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>
>
___________________________________________________________
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