Deserialize null to tool parameter default value

I'm not 100% certain about this commit, but it does make some sense:

We might be setting optional step outputs to null if they're not
provided or if they are provided as null. We do have tests that require
that tool default values are used when an optional parameter is not
provided, so it seems like this is a necessity.

The advantage is that this is pretty easy to reason about, the downside
is that you can't provide a null value to an optional parameter that
specifies a non-null default value. This might seem nonsensical at first
since you might just drop the default value, but if a tool can accept
null but the default should be not-null, you still might want to
override the default with a null (in a workflow or tool run).

An alternative fix would need to distinguish unset and null, and would
need to persist the unset value in the database, or we'd have to rework
the scheduling code so that unset step outputs don't cause scheduling
errors.

Maybe this is good enough for now ?

lib/galaxy/tools/parameters/basic.py

@@ -242,6 +242,9 @@ def to_json(self, value, app, use_security) -> str:
 
     def to_python(self, value, app):
         """Convert a value created with to_json back to an object representation"""
+        if value is None and (default_value := getattr(self, "value", None)) not in ("", None):
+            # None should be equivalent to no value provided, so use default
+            return default_value
         return value
 
     def value_to_basic(self, value, app, use_security=False):
@@ -494,6 +497,9 @@ def to_python(self, value, app):
         except (TypeError, ValueError) as err:
             if contains_workflow_parameter(value):
                 return value
+            if value is None and self.value not in ("", None):
+                # None should be equivalent to no value provided, so use default
+                return int(self.value)
             if not value and self.optional:
                 return None
             raise err
@@ -567,6 +573,9 @@ def to_python(self, value, app):
         except (TypeError, ValueError) as err:
             if contains_workflow_parameter(value):
                 return value
+            if value is None and self.value not in ("", None):
+                # None should be equivalent to no value provided, so use default
+                return float(self.value)
             if not value and self.optional:
                 return None
             raise err
@@ -623,6 +632,9 @@ def from_json(self, value, trans, other_values=None):
         return self.to_python(value)
 
     def to_python(self, value, app=None):
+        if value is None and self.checked is not None:
+            # None should be equivalent to no value provided, so use default
+            return self.checked
         if not self.optional:
             ret_val = string_as_bool(value)
         else: