Hi Christian,
Can you show the complete example tool? In particular, what is the
XML wrapper's <stdio> tag? By default Galaxy does treat anything
on stderr as an error. See:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Peter
On Thu, May 14, 2015 at 11:54 AM, Christian Brenninkmeijer
<christian.brenninkmei...@manchester.ac.uk> wrote:
> Hi,
>
> I have noticed that Planemo (0.11.1) causes tests to fail if anything is
> written to sys.error.
>
> For example if I test the following simple python:
>
> import sys
> if __name__ == '__main__':
> #sys.stderr.write("This is a test")
> print "Done"
>
> My test pass;
> But if I remove the comment:
>
> import sys
> if __name__ == '__main__':
> sys.stderr.write("This is a test")
> print "Done"
>
> The test fails!
>
> Is there a way to tell planemo that it is ok if the program writes to
> sys.error?
> Assuming of course a normal 0 exit as above.
>
> Without this it wuld be impossible to test any tool that wraps code that
> writes to sys.error such things as warning message up %done.
>
> Thanks in advance
> Christian Brenninkmeijer
> University of Manchester
>
>
>
>
>
>
>
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