Welcome, @davide_bersanetti
I think I understand your question – you want to use an option with the tool that some of the other options are incompatible with, yes?
If that is a parameter combination that is incompatible with SPAdes itself, then remember that the tool is the same in Galaxy as anywhere else. The only difference is that we put a web interface on top to make constructing the command line easier. So – increased accessibility, and the underlying algorithm is still the same.
What to do
-
Check the SPAdes tool documentation – is what you want to do possible?
-
If possible, does your query meet the requirements for that? Meaning: sometimes parameter combinations are dependent on characteristics of the input, so confirm that as well.
-
Then try to apply that logic onto the Galaxy form.
-
If you need help with any of this, you can share what you have now (screenshots?) and we can help to confirm what might be going on. Most tool forms have “every” option but there are some practical limits at the public servers. We can clarify and make development requests as appropriate.
Hope this helps!