Genome/annotation data can be pre-set within a workflow only if it is already indexed/built-in at the server you are working on. Details:
For the reference genome:
- If the genome indexed at the Galaxy server you are working at for these tools (built-in), that can be set within the Workflow editor before runtime. Click on the tool and in the right side panel the entire tool form will be available where you can pre-set the target genome build.
- If instead this is a custom genome, that will need to be a user-selected input dataset from the history and the tool forms in the workflow editor can be set up to use that custom build. Create an "input" for the fasta custom genome and connect it to the tool with a noodle.
For the reference annotation,
- Most tools require a user-selected input dataset from the history (including both Bowtie and HTseq-count)
- Annotation is linked into the workflow the same way as a custom genome: create an "input" for the reference annotation and connect it to the tool with a noodle.
Workflow "inputs" can be custom labeled to clarify which data should be selected at runtime.
Thanks! Jen, Galaxy team