Allow processing multiple files

[reckart]

The idea is to set the multiple flag on the input parameter of the engine, then in the tool XML file write all the input file names to a temporary file, and that temporary file is then passed as a parameter to the tool wrapper groovy script. The Groovy script would then read this temporary file and pass all the file names to PARAM_PATTERNS. The resulting files would then need to be discovered.

• need to check if the input files that galaxy provides are simple file names (such that we can use PARAM_SOURCE_LOCATION) or absolute files
• need to check if we can write the results all to some directory using PARAM_TARGET_LOCATION