Each row of the metadata file ("parameter file") is  an assay and it contains a name of a result file (the one used in a zip folder) or a path within a folder (in case of directory structure).

For example, if a zip folder named "a.zip" contains:

- data1.txt
- subdir/data2.txt
- subdir/subdir2/data1.txt

Parameter file should refer to data files as "data1.txt", "subdir/data2.txt", "subdir/subdir2/data1.txt".

This will provide the necessary link between experiment annotation and the data itself.
The metadata file also can provide a third level id from SIMS (for instance, an aliquot id), and all other parameters which a user might want to submit.