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do not print newlines to stderr

Matthias Bernt requested to merge Bernt/proteinortho:Bernt-master-patch-25540 into master

The redirection (2>&1) over here https://github.com/galaxyproject/tools-iuc/blob/d9cb4478858f60aacb8577eb16e291961384eb1c/tools/proteinortho/proteinortho_summary.xml#L14 is a bit annoying, since we also loose error messages.

Edited by Matthias Bernt

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