Treatment of tools is inconsistent between the GUI layer and the command line.
Certain tool wrappers define a default parameter which on the command line is sent as "no value" (ie no flag at all) still requires a choice to be made on the GUI level. This is problematic when managing tools through the API. Currently Galaksio checks if a required field is empty when importing the workflow JSON from Galaxy and then interprets the required field as optional (in the Galaksio GUI this mean that the default "no value" is pre-selected but any value is accepted).
This does however not work if a Galaxy workflow has been made with a non-default value in a tool which got a required field and where the default value is sent as "no value". Because in such cases the default value is still interpreted as not filling in a required field.
Treatment of tools is inconsistent between the GUI layer and the command line.
Certain tool wrappers define a default parameter which on the command line is sent as "no value" (ie no flag at all) still requires a choice to be made on the GUI level. This is problematic when managing tools through the API. Currently Galaksio checks if a required field is empty when importing the workflow JSON from Galaxy and then interprets the required field as optional (in the Galaksio GUI this mean that the default "no value" is pre-selected but any value is accepted).
This does however not work if a Galaxy workflow has been made with a non-default value in a tool which got a required field and where the default value is sent as "no value". Because in such cases the default value is still interpreted as not filling in a required field.