To transform your data you don't need to load all of it into HALE. Usually it's a better practice to only load a representative sample of your data, to help you verify the mapping and quickly get feedback on its transformation. Once you have defined the mapping you have the possibility to transform your data without loading it into the project, but launching a dedicated data transformation job.
To transform external data, select Transformation→Transform external data... from the main menu. Next you will be prompted to select source data files that you want to use. Click on Add source file to add another file. The instance import wizard will open for you to select the file of your choice. After adding at least one file you can proceed to select the target file as in the transformed data export wizard.
If your alignment only contains one-to-one type relations, e.g. Retype,
the data will directly be transformed and streamed from the data source to the target file.
If you also use for example Merge or Join the source data will first be read into a temporary database for performance reasons.