The EU does not allow business method patents, which is what most people actually mean when they say "software patents". It does allow computer algorithm patents.
That "very plain language" only excludes business method patents i.e. "...on a computer" or "...on the internet" patents. These are not computer algorithm patents (for example, a new sorting or encryption algorithm). The term "software patent" does not denote a distinct class of patent.
Computer algorithms are patentable in the EU. I can think of many, many examples of computer algorithms that are patented in the EU (e.g. crypto patents, compression algorithms, codecs, etc.).
Patents have certainly been granted, but the language I link to above is very clear about the validity of such patents:
"The following in particular shall not be regarded as inventions [...]: schemes, rules and methods for performing mental acts, playing games or doing business, and programs for computers."
