Hi @maham_hamid & thanks for posting this to the forum!
In short, for these tools, as installed at https://usegalaxy.eu:
Using a Custom reference genome fasta might work with both of the “Genome” inputs. It depends on your reference genome. Larger genomes are sometimes problematic (are too large to process against). Smaller genomes would likely work fine.
The first FAQ covers how to format a reference genome/transcriptome/exome used from the history. The second covers some common issues people encounter when mixing natively indexed genomes with custom genomes or externally mapped data or when incorporating other inputs (reference annotation, etc).
ping @hxr @bjoern.gruening for advice about usage and future plans for indexes. Maybe we could reach out to the tool authors and see if they can update the tools to use the genomes already indexed on a server for this type of input? (“all_fasta” data table ??).
A few other tools have needed changes around using build-in indexes (were initially pulling data from a tool-specific data table, instead of a global data table) but I can’t remember exactly how at the end that was remedied – tool wrapper update or a Galaxy update/config change? Thanks & we can ping the authors at their development repository (once clarified && if needed).