I think that there is difficulty adding synteny tracks a lot of the time because we are not explicit about what is the query assembly and what is the target assembly (for the types of alignments where this matters)
This applies to both the CLI and the UI
This should get updated. In the GUI, it might need to be that we explicitly use the terminology query and target (perhaps except for the MCScan, where that is less well defined, needs review)
And in the CLI, possibly adding a separate "add-synteny-track" CLI could allow this to be more simple than overloading add-track with more options
I think that there is difficulty adding synteny tracks a lot of the time because we are not explicit about what is the query assembly and what is the target assembly (for the types of alignments where this matters)
This applies to both the CLI and the UI
This should get updated. In the GUI, it might need to be that we explicitly use the terminology query and target (perhaps except for the MCScan, where that is less well defined, needs review)
And in the CLI, possibly adding a separate "add-synteny-track" CLI could allow this to be more simple than overloading add-track with more options