OK I never use an IDE or even Sharepoint to directly pull data so I really don't know the answer to your specific problem. (Incidentally that XML you posted looks just like a "log in" XML and nothing to do with a query call at all)
However what you are using here (in Clarity terms) is the "query API" and so I'd check the documentation ; eg
HERE and any other discussions on these boards about "query API" for clues.
The confusing thing that you might not expect if you understand all that WSDL business is that (to me, from a position of relative ignorance about these things) what Clarity gives you (i.e. what is exposed on that .../niku/wsdl/query URL) is itself, not much use - but I do know that if you construct SOAP messages and use the relevant XML (as per the documentation) it all works fine.
(i.e. the .../niku/wsdl/query stuff does not really tell you how to consume the service, but the common "call a query" XML code works for any of the queries exposed on that URL)