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.brenninkmeijer@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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