Hello,
How the data is consumed is explained on the tool form in the data entry area. Please review how to interpret this below and let us know if you are not sure about a particular tool. We might be able to explain how to access the help, or the tool might need an update to make the usage clearer.
Example1: Samtools Sort > click on the Multiple Dataset or Dataset Collection icons and this new help text will be presented: This is a batch mode input field. Separate jobs will be triggered for each dataset selection.
Example2: Samtools Mpileup > multiple dataset selection is the default (one or more can be chosen), or click to Collections where one or more can be selected. No new help text is presented to warn about the batch job mode. This means that inputs are processed together in the same job.
More complex entry can be found on tools like Compare two Datasets, where there are two input sections and each can have a single or multiple (batch) entry (individually selected or in a collection). The batch mode help text comes up when multiple/collections are selected. This is expanded behavior similar to Sort above.
And even more complex entry can be found on tools like MultiQC, where one or more input sets can be selected, and additional input sets (Reports) sections can be optionally added in. There is no batch mode entry text reported, meaning that all data is run with the same job. This is expanded behavior similar to Mpileup above, where each subsection is combined to produce a summary sub-report, then the final results from each sub-report is combined into the final report.
Hope that helps!