I'm working with a lab doing research with bacterial genomes and I'm working on introducing their pipeline into Galaxy. In many cases the bacterial data consists of a combination of species, so mapping to a specific genome is tricky.
Mapping bacterial data to a referencce genome has 3 options:
the genome is known, so is selected from local cache as is often done in Galaxy
a custom reference is selected - these custom references are a composition of files, and I'm not aware if/how this is currently handled in Galaxy. For example, for the custom reference for Brucella_abortus1 consists of the following 7 files:
The input data is inspected to determine the optimal genome to be mapped.
Does anyone know if this is currently being done in Galaxy? I've done some searching and only found this so far https://help.galaxyproject.org/t/mapping-rna-seq-data-to-a-composite-build-of-bacterial-genomes/1443.
I can wrap the tool for Galaxy that the lab is using, but I want to make sure I'm not re-inventing the wheel.
select tsv data sets(s)
iqtreeto handle custom models correctly: galaxyproject/tools-iuc#2835