Some questions before updating the Galaxy Wrapper to 5.5.0

[Stephan Flemming]

Hi,

I want to update the Galaxy wrapper to 5.5.0 and I have some basic questions.

https://github.com/galaxyproject/tools-iuc/blob/master/tools/transdecoder/transdecoder.xml

The current version merges LongOrfs and Predict and therefore both commands are always used together. Following the instructions in the Wiki, there is a homology search step in between, that was maybe not yet implemented in 3.0.1. Do you recommend splitting these two sub commands into two wrappers? I don't have much experience with TransDecoder and I am not even sure, if the LongOrfs and Predict step will ever be used separately.

The current wrapper uses a parameter --cpu that is not listed in --help. Is it still available?

The --help mentions -G and --genetic_code. What is the difference? And since LongOrfs and Predict can use them, is it useful or even allowed that both commands use a different value? Or is this some kind of shared parameter?

Thanks in advance,

Stephan