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Fix generation of parameter file for selecting the output

Loic Hausammann requested to merge select_output into master

Hi,

I am just moving around a bit of code (and clarifying the help).

Currently we cannot use swift like this ./swift -o test.yml to generate a parameters file with all the options related to the output selection. The code fails because it did not received a parameter file.

Therefore I moved the piece of code that generates the output file before the check for the arguments.

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