Major The validation message may not give a relevant information:
Case 1: In the "Find Patterns" sample setup inputs and outputs. Press the validate button. The message says: "Scheme is valid" yet there are warning: "...Warning empty input slot: Plain text". The message must say "The scheme is valid. There are non-critical warnings".
Case 2: External tools may have path but be invalid. There must be a warning "External tool is invalid. UGENE may not support this version of the tool or a wrong path to the tools is selected".