diff --git a/client/src/components/Tool/ToolFooter.vue b/client/src/components/Tool/ToolFooter.vue
index 6766a8ffa0f..d7775129712 100644
--- a/client/src/components/Tool/ToolFooter.vue
+++ b/client/src/components/Tool/ToolFooter.vue
@@ -40,7 +40,7 @@
             <span v-localize class="footer-section-name">References</span>
             <div v-for="(xref, index) in xrefs" :key="index">
                 -
-                <template v-if="xref.reftype == 'bio.tools'">
+                <template v-if="xref.type == 'bio.tools'">
                     bio.tools: {{ xref.value }} (<a :href="`https://bio.tools/${xref.value}`" target="_blank"
                         >bio.tools
                         <FontAwesomeIcon
@@ -55,13 +55,13 @@
                             icon="external-link-alt" /> </a
                     >)
                 </template>
-                <template v-else-if="xref.reftype == 'bioconductor'">
+                <template v-else-if="xref.type == 'bioconductor'">
                     Bioconductor Package:
                     <a :href="`https://bioconductor.org/packages/${xref.value}/`" target="_blank"
                         >{{ xref.value }} (doi:10.18129/B9.bioc.{{ xref.value }})</a
                     >
                 </template>
-                <template v-else> {{ xref.reftype }}: {{ xref.value }} </template>
+                <template v-else> {{ xref.type }}: {{ xref.value }} </template>
             </div>
         </div>
         <div v-if="hasCreators" class="mb-1">
diff --git a/lib/galaxy/tool_util/linters/general.py b/lib/galaxy/tool_util/linters/general.py
index eb3a98fd3b8..cd726fa9d37 100644
--- a/lib/galaxy/tool_util/linters/general.py
+++ b/lib/galaxy/tool_util/linters/general.py
@@ -237,7 +237,7 @@ class BioToolsValid(Linter):
         _, tool_node = _tool_xml_and_root(tool_source)
         xrefs = tool_source.parse_xrefs()
         for xref in xrefs:
-            if xref["reftype"] != "bio.tools":
+            if xref["type"] != "bio.tools":
                 continue
             metadata_source = ApiBiotoolsMetadataSource()
             if not metadata_source.get_biotools_metadata(xref["value"]):
diff --git a/lib/galaxy/tool_util/ontologies/ontology_data.py b/lib/galaxy/tool_util/ontologies/ontology_data.py
index 65343a803c3..89ee0e72999 100644
--- a/lib/galaxy/tool_util/ontologies/ontology_data.py
+++ b/lib/galaxy/tool_util/ontologies/ontology_data.py
@@ -53,7 +53,7 @@ class OntologyData(NamedTuple):
 
 def biotools_reference(xrefs):
     for xref in xrefs:
-        if xref["reftype"] == "bio.tools":
+        if xref["type"] == "bio.tools":
             return xref["value"]
     return None
 
@@ -69,11 +69,11 @@ def expand_ontology_data(
     tool_source: ToolSource, all_ids: List[str], biotools_metadata_source: Optional[BiotoolsMetadataSource]
 ) -> OntologyData:
     xrefs = tool_source.parse_xrefs()
-    has_biotools_reference = any(x["reftype"] == "bio.tools" for x in xrefs)
+    has_biotools_reference = any(x["type"] == "bio.tools" for x in xrefs)
     if not has_biotools_reference:
         for legacy_biotools_ref in legacy_biotools_external_reference(all_ids):
             if legacy_biotools_ref is not None:
-                xrefs.append({"value": legacy_biotools_ref, "reftype": "bio.tools"})
+                xrefs.append({"value": legacy_biotools_ref, "type": "bio.tools"})
 
     edam_operations = tool_source.parse_edam_operations()
     edam_topics = tool_source.parse_edam_topics()
diff --git a/lib/galaxy/tool_util/parser/cwl.py b/lib/galaxy/tool_util/parser/cwl.py
index 77066125dee..00ce4738eab 100644
--- a/lib/galaxy/tool_util/parser/cwl.py
+++ b/lib/galaxy/tool_util/parser/cwl.py
@@ -159,7 +159,7 @@ class CwlToolSource(ToolSource):
             output.format = "expression.json"
         output.change_format = []
         output.format_source = None
-        output.metadata_source = ""
+        output.metadata_source = None
         output.parent = None
         output.label = None
         output.count = None
diff --git a/lib/galaxy/tool_util/parser/output_collection_def.py b/lib/galaxy/tool_util/parser/output_collection_def.py
index b588957d651..f5c279dd372 100644
--- a/lib/galaxy/tool_util/parser/output_collection_def.py
+++ b/lib/galaxy/tool_util/parser/output_collection_def.py
@@ -58,7 +58,7 @@ def dataset_collector_descriptions_from_elem(elem, legacy=True):
 
 
 def dataset_collector_descriptions_from_output_dict(as_dict):
-    discover_datasets_dicts = as_dict.get("discover_datasets", [])
+    discover_datasets_dicts = as_dict.get("discover_datasets") or []
     if is_dict(discover_datasets_dicts):
         discover_datasets_dicts = [discover_datasets_dicts]
     dataset_collector_descriptions = dataset_collector_descriptions_from_list(discover_datasets_dicts)
diff --git a/lib/galaxy/tool_util/parser/output_objects.py b/lib/galaxy/tool_util/parser/output_objects.py
index 86a627d15de..090b38ac63b 100644
--- a/lib/galaxy/tool_util/parser/output_objects.py
+++ b/lib/galaxy/tool_util/parser/output_objects.py
@@ -175,24 +175,25 @@ class ToolOutput(ToolOutputBase):
             hidden=self.hidden,
             format=self.format,
             format_source=self.format_source,
-            metadata_source=self.metadata_source or None,  # model is decorated as Optional
+            metadata_source=self.metadata_source,
             discover_datasets=[d.to_model() for d in self.dataset_collector_descriptions],
+            from_work_dir=self.from_work_dir,
         )
 
     @staticmethod
     def from_dict(name: str, output_dict: Dict[str, Any], app: Optional[ToolOutputActionApp] = None) -> "ToolOutput":
         output = ToolOutput(name)
-        output.format = output_dict.get("format", "data")
+        output.format = output_dict.get("format") or "data"
         output.change_format = []
-        output.format_source = output_dict.get("format_source", None)
-        output.default_identifier_source = output_dict.get("default_identifier_source", None)
-        output.metadata_source = output_dict.get("metadata_source", "")
-        output.parent = output_dict.get("parent", None)
-        output.label = output_dict.get("label", None)
+        output.format_source = output_dict.get("format_source")
+        output.default_identifier_source = output_dict.get("default_identifier_source")
+        output.metadata_source = output_dict.get("metadata_source")
+        output.parent = output_dict.get("parent")
+        output.label = output_dict.get("label")
         output.count = output_dict.get("count", 1)
         output.filters = []
-        output.from_work_dir = output_dict.get("from_work_dir", None)
-        output.hidden = output_dict.get("hidden", False)
+        output.from_work_dir = output_dict.get("from_work_dir")
+        output.hidden = output_dict.get("hidden") or False
         # TODO: implement tool output action group fixes
         if app is not None:
             output.actions = ToolOutputActionGroup(app, None)
diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index bbff153fd55..1b942b3070a 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -224,7 +224,7 @@ class XmlToolSource(ToolSource):
         if xrefs is None:
             return []
         return [
-            XrefDict(value=xref.text.strip(), reftype=str(xref.attrib["type"]))
+            XrefDict(value=xref.text.strip(), type=str(xref.attrib["type"]))
             for xref in xrefs.findall("xref")
             if xref.get("type") and xref.text
         ]
@@ -489,7 +489,7 @@ class XmlToolSource(ToolSource):
                 inherit_format = string_as_bool(collection_elem.get("inherit_format", None))
                 inherit_metadata = string_as_bool(collection_elem.get("inherit_metadata", None))
             default_format_source = collection_elem.get("format_source", None)
-            default_metadata_source = collection_elem.get("metadata_source", "")
+            default_metadata_source = collection_elem.get("metadata_source", None)
             filters = collection_elem.findall("filter")
 
             dataset_collector_descriptions = None
@@ -560,7 +560,7 @@ class XmlToolSource(ToolSource):
         app: Optional[ToolOutputActionApp] = None,
         default_format="data",
         default_format_source=None,
-        default_metadata_source="",
+        default_metadata_source=None,
         expression_type=None,
     ):
         from_expression = data_elem.get("from")
diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index 3ae32c643f1..b2c734f7979 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -86,7 +86,7 @@ class YamlToolSource(ToolSource):
 
     def parse_xrefs(self) -> List[XrefDict]:
         xrefs = self.root_dict.get("xrefs", [])
-        return [XrefDict(value=xref["value"], reftype=xref["type"]) for xref in xrefs if xref["type"]]
+        return [XrefDict(value=xref["value"], type=xref["type"]) for xref in xrefs if xref["type"]]
 
     def parse_sanitize(self):
         return self.root_dict.get("sanitize", True)
@@ -192,7 +192,7 @@ class YamlToolSource(ToolSource):
             inherit_format = output_dict.get("inherit_format", None)
             inherit_metadata = output_dict.get("inherit_metadata", None)
         default_format_source = output_dict.get("format_source", None)
-        default_metadata_source = output_dict.get("metadata_source", "")
+        default_metadata_source = output_dict.get("metadata_source", None)
         filters = []
         dataset_collector_descriptions = dataset_collector_descriptions_from_output_dict(output_dict)
 
diff --git a/lib/galaxy/tool_util_models/tool_outputs.py b/lib/galaxy/tool_util_models/tool_outputs.py
index 322f338aa06..0c686fdfaa3 100644
--- a/lib/galaxy/tool_util_models/tool_outputs.py
+++ b/lib/galaxy/tool_util_models/tool_outputs.py
@@ -33,6 +33,7 @@ class ToolOutputDataset(ToolOutputBaseModel):
     format_source: Optional[str]
     metadata_source: Optional[str]
     discover_datasets: Optional[List["DatasetCollectionDescriptionT"]]
+    from_work_dir: Optional[str] = None
 
 
 class ToolOutputCollectionStructure(BaseModel):
diff --git a/lib/galaxy/tool_util_models/tool_source.py b/lib/galaxy/tool_util_models/tool_source.py
index 487870895bd..d7bb207b58d 100644
--- a/lib/galaxy/tool_util_models/tool_source.py
+++ b/lib/galaxy/tool_util_models/tool_source.py
@@ -15,7 +15,7 @@ from typing_extensions import (
 
 class XrefDict(TypedDict):
     value: str
-    reftype: str
+    type: str
 
 
 class Citation(BaseModel):
diff --git a/lib/galaxy_test/api/test_tools.py b/lib/galaxy_test/api/test_tools.py
index bb7a2cb1330..59f34dd9b79 100644
--- a/lib/galaxy_test/api/test_tools.py
+++ b/lib/galaxy_test/api/test_tools.py
@@ -257,7 +257,7 @@ class TestToolsApi(ApiTestCase, TestsTools):
         assert "xrefs" in get_json
         assert len(get_json["xrefs"]) == 1
         xref = get_json["xrefs"][0]
-        assert xref["reftype"] == "bio.tools"
+        assert xref["type"] == "bio.tools"
         assert xref["value"] == "bwa"
 
     @skip_without_tool("test_data_source")
diff --git a/lib/tool_shed/webapp/frontend/src/components/pages/ToolVersionPage.vue b/lib/tool_shed/webapp/frontend/src/components/pages/ToolVersionPage.vue
index 1adaa1b5c52..7ebe291bc1b 100644
--- a/lib/tool_shed/webapp/frontend/src/components/pages/ToolVersionPage.vue
+++ b/lib/tool_shed/webapp/frontend/src/components/pages/ToolVersionPage.vue
@@ -156,11 +156,11 @@ const linkedFromOlderRevision = computed(() => {
                 <q-list bordered separator>
                     <q-item v-for="xref in xrefs" :key="xref.value">
                         <q-item-section>
-                            <q-item-label overline>REFERENCE {{ xref.reftype }}</q-item-label>
-                            <q-item-label v-if="xref.reftype == 'bio.tools'">
+                            <q-item-label overline>REFERENCE {{ xref.type }}</q-item-label>
+                            <q-item-label v-if="xref.type == 'bio.tools'">
                                 <bio-tools-link :id="xref.value" />
                             </q-item-label>
-                            <q-item-label v-else-if="xref.reftype == 'bioconductor'">
+                            <q-item-label v-else-if="xref.type == 'bioconductor'">
                                 <bioconductor-link :id="xref.value" />
                             </q-item-label>
                             <q-item-label v-else>
diff --git a/lib/tool_shed/webapp/frontend/src/schema/schema.ts b/lib/tool_shed/webapp/frontend/src/schema/schema.ts
index d78c4048d87..52b5aaaec81 100644
--- a/lib/tool_shed/webapp/frontend/src/schema/schema.ts
+++ b/lib/tool_shed/webapp/frontend/src/schema/schema.ts
@@ -2727,6 +2727,8 @@ export interface components {
             format: string
             /** Format Source */
             format_source: string | null
+            /** From Work Dir */
+            from_work_dir?: string | null
             /** Hidden */
             hidden: boolean
             /** Label */
@@ -3006,8 +3008,8 @@ export interface components {
         }
         /** XrefDict */
         XrefDict: {
-            /** Reftype */
-            reftype: string
+            /** Type */
+            type: string
             /** Value */
             value: string
         }
diff --git a/test/unit/tool_util/test_ontologies.py b/test/unit/tool_util/test_ontologies.py
index 5c1faca4771..15873910a77 100644
--- a/test/unit/tool_util/test_ontologies.py
+++ b/test/unit/tool_util/test_ontologies.py
@@ -87,7 +87,7 @@ def test_parse_edam_mapping_operations_legacy():
 def test_parse_biotools_default_mapping():
     test_source = get_test_tool_source(source_file_name="testtool.yml", source_contents=TOOL_YAML_NO_EXPLICIT_XREFS)
     ontology_data = expand_ontology_data(test_source, ["cheetah_problem_unbound_var_input"], None)
-    assert ontology_data.xrefs[0]["reftype"] == "bio.tools"
+    assert ontology_data.xrefs[0]["type"] == "bio.tools"
     assert ontology_data.xrefs[0]["value"] == "bwa"
 
     test_source = get_test_tool_source(source_file_name="testtool.yml", source_contents=TOOL_YAML_NO_EXPLICIT_XREFS)
diff --git a/test/unit/tool_util/test_parsing.py b/test/unit/tool_util/test_parsing.py
index 2c57377db14..8698be752fe 100644
--- a/test/unit/tool_util/test_parsing.py
+++ b/test/unit/tool_util/test_parsing.py
@@ -416,7 +416,7 @@ class TestXmlLoader(BaseLoaderTestCase):
 
     def test_xrefs(self):
         xrefs = self._tool_source.parse_xrefs()
-        assert xrefs == [{"value": "bwa", "reftype": "bio.tools"}]
+        assert xrefs == [{"value": "bwa", "type": "bio.tools"}]
 
     def test_exit_code(self):
         tool_source = self._get_tool_source(
@@ -622,7 +622,7 @@ class TestYamlLoader(BaseLoaderTestCase):
 
     def test_xrefs(self):
         xrefs = self._tool_source.parse_xrefs()
-        assert xrefs == [{"value": "bwa", "reftype": "bio.tools"}]
+        assert xrefs == [{"value": "bwa", "type": "bio.tools"}]
 
     def test_sanitize(self):
         assert self._tool_source.parse_sanitize() is True