Generally, there are no restrictions on file formats in Standardizer. Every file format that is supported by JChem/Marvin can be used within Standardizer, too.
Multiple files can be specified as an input that can differ in their molecular file formats as well.
In every case, a single output file is generated with the requested molecular file format.
File format flexibility also allows concatenating molecule files and/or export to another format by leaving standardization rules empty.