Most tool forms include all three of Galaxy's options for input selection. For example, the tool EMBOSS: sixpack has an input on the tool form named Sequences (with expected the format/datatype of "fasta") and it includes these buttons:
- The first button is used to input a single dataset
- The second button is used to input multiple individual datasets
- The third button is to input a dataset collection (multiple individual datasets in one or more defined groups, termed "collections")
Hover over the buttons to view the pop-up labels and click on one to make the choice. Datasets or dataset collections with the expected input format set as the datatype can then be selected/multi-selected.
The second or third option is considered batch processing. A distinct job will be run for each individual input fasta dataset contained within the batch with a single "Execute" click.
This is a good question and may help others, too.
Best, Jen, Galaxy team