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 jmchilton@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 ngsbioinformatics@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.baker@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 ngsbioinformatics@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.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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