matchms: switch to scores object

[hechth]

Currently, the matchms similarity tool creates 2 tables containing the matches and scores tables - with the newer 2.5d scores arrays that are in progress here and here, it is better to stick with the Scores object also in Galaxy and create tools for plotting, exporting or filtering inside Galaxy as well, creating a set of simpler, modular tools.

This also means changing the input for the matchms formatting tool which currently takes 2 tables as input - this can then directly take a score as input.