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:
myself. Björn Grüning uses -
which is a popular choice.
As a heads up for people reading discussion in the future - starting
in 15.05 - you will be able
Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or 2
fastq files as input. If 1 file is specified, then 1 output file is
created. If 2 inputs are specified, then 2 output files will be created.
How do I specify the optional output parameter?
I'm using this as my tool descrip
this works. Thanks.
On Tue, Apr 28, 2015 at 11:51 AM, Dannon Baker
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, A
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 wrote:
> ok, thanks. Let me look at this. When I look at the info
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
wrote:
> You probably need to set the tag, since due to a
> histo
You probably need to set the 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 wrote:
> Hi - I implemented a tool I us into Galaxy
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,
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
