diff --git a/client/src/components/Collections/BuildFileSetWizard.vue b/client/src/components/Collections/BuildFileSetWizard.vue
index 35b2d964ace..258b9531677 100644
--- a/client/src/components/Collections/BuildFileSetWizard.vue
+++ b/client/src/components/Collections/BuildFileSetWizard.vue
@@ -1,5 +1,5 @@
 <script setup lang="ts">
-import { BCardGroup } from "bootstrap-vue";
+import { BAlert, BCardGroup } from "bootstrap-vue";
 import { computed, ref } from "vue";
 
 import { GalaxyApi } from "@/api";
@@ -11,6 +11,7 @@ import { forBuilder, type ForBuilderResponse } from "@/components/Collections/wi
 import { useWizard } from "@/components/Common/Wizard/useWizard";
 import { useToolRouting } from "@/composables/route";
 import localize from "@/utils/localization";
+import { errorMessageAsString } from "@/utils/simple-error";
 
 import type {
     ParsedFetchWorkbook,
@@ -112,7 +113,7 @@ const wizard = useWizard({
     },
     "upload-workbook": {
         label: "Upload workbook",
-        instructions: "Upload a workbook containing with URIs and metadata",
+        instructions: "Upload a workbook containing URIs with metadata",
         isValid: () => sourceFrom.value === "workbook" && workbookCompleted.value,
         isSkippable: () => sourceFrom.value !== "workbook",
     },
@@ -238,7 +239,7 @@ async function handleWorkbook(base64Content: string) {
         handleUploadedData(data);
     } else {
         console.log(error);
-        uploadErrorMessage.value = "There was an error processing the file.";
+        uploadErrorMessage.value = "There was an error processing the file. " + errorMessageAsString(error);
     }
 }
 
@@ -259,17 +260,26 @@ const {
 <template>
     <GenericWizard :use="wizard" :submit-button-label="importButtonLabel" :title="title" @submit="submit">
         <template v-slot:header>
+            <BAlert
+                :show="!!uploadErrorMessage"
+                variant="danger"
+                class="my-2"
+                dismissible
+                @dismissed="uploadErrorMessage = ''">
+                {{ uploadErrorMessage }}
+            </BAlert>
             <h2 data-galaxy-file-drop-target>
                 {{ title }}
-                <FontAwesomeIcon
-                    class="workbook-upload-helper mr-1"
-                    :class="dropZoneClasses"
-                    :title="dropWorkbookTitle"
-                    :icon="faUpload"
-                    @click.prevent="browseFiles"
-                    @drop.prevent="handleDrop"
-                    @dragover.prevent="isDragging = true"
-                    @dragleave.prevent="isDragging = false" />
+                <a v-b-tooltip.hover aria-label="Upload Completed Workbook" :title="dropWorkbookTitle" href="#">
+                    <FontAwesomeIcon
+                        class="workbook-upload-helper mr-1"
+                        :class="dropZoneClasses"
+                        :icon="faUpload"
+                        @click.prevent="browseFiles"
+                        @drop.prevent="handleDrop"
+                        @dragover.prevent="isDragging = true"
+                        @dragleave.prevent="isDragging = false" />
+                </a>
                 <HiddenWorkbookUploadInput ref="uploadRef" @onFileUpload="onFileUpload" />
             </h2>
         </template>
@@ -336,5 +346,8 @@ const {
 // modeled a bit after upload-helper in the upload component...
 .workbook-upload-helper {
     color: $border-color;
+    &:hover {
+        color: $brand-primary;
+    }
 }
 </style>
diff --git a/client/src/components/Collections/wizard/CardDownloadWorkbook.vue b/client/src/components/Collections/wizard/CardDownloadWorkbook.vue
index 110fbf7c832..9b638b161c3 100644
--- a/client/src/components/Collections/wizard/CardDownloadWorkbook.vue
+++ b/client/src/components/Collections/wizard/CardDownloadWorkbook.vue
@@ -3,6 +3,16 @@ import { faDownload } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BCard, BCardTitle, BLink } from "bootstrap-vue";
 
+// We use this in two capacities - one where we have to do a post and do complex things
+// to generate the workbook and one where we just have an easy link. Support both.
+interface Props {
+    generateWorkbookLink?: string;
+}
+
+withDefaults(defineProps<Props>(), {
+    generateWorkbookLink: undefined,
+});
+
 const emit = defineEmits(["download"]);
 </script>
 
@@ -11,6 +21,8 @@ const emit = defineEmits(["download"]);
         <BCardTitle>
             <b>Step 1: Download</b>
         </BCardTitle>
-        <BLink @click="emit('download')"><FontAwesomeIcon size="xl" :icon="faDownload" /> Download workbook.</BLink>
+        <BLink :href="generateWorkbookLink" @click="emit('download')"
+            ><FontAwesomeIcon size="xl" :icon="faDownload" /> Download workbook.</BLink
+        >
     </BCard>
 </template>
diff --git a/client/src/components/Collections/wizard/HiddenWorkbookUploadInput.vue b/client/src/components/Collections/wizard/HiddenWorkbookUploadInput.vue
index 0e54ba459dc..8760e308d63 100644
--- a/client/src/components/Collections/wizard/HiddenWorkbookUploadInput.vue
+++ b/client/src/components/Collections/wizard/HiddenWorkbookUploadInput.vue
@@ -19,6 +19,6 @@ defineExpose({
 
 <template>
     <label style="display: none">
-        <input ref="fileInputRef" type="file" accept=".xlsx" @change="onFileUpload" />
+        <input ref="fileInputRef" type="file" accept=".xlsx,.xls,.tsv,.csv,.tabular" @change="onFileUpload" />
     </label>
 </template>
diff --git a/client/src/components/Collections/wizard/fetchWorkbooks.ts b/client/src/components/Collections/wizard/fetchWorkbooks.ts
index 774e1668f8b..cc972662ed9 100644
--- a/client/src/components/Collections/wizard/fetchWorkbooks.ts
+++ b/client/src/components/Collections/wizard/fetchWorkbooks.ts
@@ -88,7 +88,9 @@ const COLUMN_TITLE_PREFIXES: Record<string, ColumnMappingType> = {
     deferredurl: "url_deferred",
     genome: "dbkey",
     dbkey: "dbkey",
+    build: "dbkey",
     filetype: "file_type",
+    type: "file_type",
     extension: "file_type",
     info: "info",
     tag: "tags",
diff --git a/client/src/components/Tool/ToolForm.vue b/client/src/components/Tool/ToolForm.vue
index 47c082d0e17..742a5c368dc 100644
--- a/client/src/components/Tool/ToolForm.vue
+++ b/client/src/components/Tool/ToolForm.vue
@@ -393,9 +393,9 @@ export default {
                 tool_id: this.formConfig.id,
                 tool_version: this.formConfig.version,
                 tool_uuid: this.toolUuid,
+                __tags: this.tags,
                 inputs: {
                     ...this.formData,
-                    __tags: this.tags,
                 },
             };
             if (this.useEmail) {
diff --git a/client/src/components/ToolsList/ToolsList.vue b/client/src/components/ToolsList/ToolsList.vue
index 94bb9e0da44..d210eecd625 100644
--- a/client/src/components/ToolsList/ToolsList.vue
+++ b/client/src/components/ToolsList/ToolsList.vue
@@ -257,43 +257,43 @@ function onToggleView(newView: ListViewMode) {
                 </GButton>
             </div>
 
-            <div class="d-flex justify-content-between align-items-center">
-                <ToolsListSectionFilters
-                    :filter-class="ToolFilters"
-                    :filter-text="filterText"
-                    :disabled="loading"
-                    @apply-filter="applyFilter" />
+            <ToolsListSectionFilters
+                :filter-class="ToolFilters"
+                :filter-text="filterText"
+                :disabled="loading"
+                @apply-filter="applyFilter">
+                <template v-slot:list-view-controls>
+                    <!-- TODO: This div here and in ListHeader.vue needs to be a reusable component -->
+                    <div class="d-flex flex-gapx-1 align-items-center">
+                        Display:
+                        <GButtonGroup>
+                            <GButton
+                                id="view-grid"
+                                tooltip
+                                title="Grid view"
+                                size="small"
+                                :pressed="currentListViewMode === 'grid'"
+                                outline
+                                color="blue"
+                                @click="onToggleView('grid')">
+                                <FontAwesomeIcon :icon="faGripVertical" />
+                            </GButton>
 
-                <!-- TODO: This div here and in ListHeader.vue needs to be a reusable component -->
-                <div>
-                    Display:
-                    <GButtonGroup>
-                        <GButton
-                            id="view-grid"
-                            tooltip
-                            title="Grid view"
-                            size="small"
-                            :pressed="currentListViewMode === 'grid'"
-                            outline
-                            color="blue"
-                            @click="onToggleView('grid')">
-                            <FontAwesomeIcon :icon="faGripVertical" />
-                        </GButton>
-
-                        <GButton
-                            id="view-list"
-                            tooltip
-                            title="List view"
-                            size="small"
-                            :pressed="currentListViewMode === 'list'"
-                            outline
-                            color="blue"
-                            @click="onToggleView('list')">
-                            <FontAwesomeIcon :icon="faBars" />
-                        </GButton>
-                    </GButtonGroup>
-                </div>
-            </div>
+                            <GButton
+                                id="view-list"
+                                tooltip
+                                title="List view"
+                                size="small"
+                                :pressed="currentListViewMode === 'list'"
+                                outline
+                                color="blue"
+                                @click="onToggleView('list')">
+                                <FontAwesomeIcon :icon="faBars" />
+                            </GButton>
+                        </GButtonGroup>
+                    </div>
+                </template>
+            </ToolsListSectionFilters>
         </div>
 
         <div class="tools-list-body">
diff --git a/client/src/components/ToolsList/ToolsListSectionFilters.vue b/client/src/components/ToolsList/ToolsListSectionFilters.vue
index 909afd4398d..32aa056eac5 100644
--- a/client/src/components/ToolsList/ToolsListSectionFilters.vue
+++ b/client/src/components/ToolsList/ToolsListSectionFilters.vue
@@ -99,134 +99,147 @@ function searchWithinSections(sections: ToolSection[], query: string) {
 
 <template>
     <div class="d-flex flex-column flex-gapy-1">
-        <div class="d-flex flex-gapx-1">
-            <BDropdown
-                block
-                :disabled="props.disabled"
-                variant="link"
-                class="tool-section-dropdown"
-                toggle-class="text-decoration-none"
-                role="menu"
-                aria-label="Select a tool section to filter by"
-                size="sm">
-                <template v-slot:button-content>
-                    <span class="sr-only">Select a tool section to filter by</span>
-                    <FontAwesomeIcon :icon="faLayerGroup" />
-                    <span v-if="selectedSection">
-                        {{ selectedSection.name }}
-                    </span>
-                    <i v-else> Select a section to filter by </i>
-                </template>
-
-                <BDropdownGroup id="searchable-sections" class="sections-select-list" header-classes="search-header">
-                    <template v-slot:header>
-                        <BDropdownText>
-                            <BFormInput
-                                v-model="defaultToolSectionsFilter"
-                                type="text"
-                                placeholder="Filter sections..." />
-                        </BDropdownText>
+        <div class="d-flex justify-content-between align-items-center">
+            <div class="d-flex flex-gapx-1">
+                <BDropdown
+                    block
+                    :disabled="props.disabled"
+                    variant="link"
+                    class="tool-section-dropdown"
+                    toggle-class="text-decoration-none"
+                    role="menu"
+                    aria-label="Select a tool section to filter by"
+                    size="sm">
+                    <template v-slot:button-content>
+                        <span class="sr-only">Select a tool section to filter by</span>
+                        <FontAwesomeIcon :icon="faLayerGroup" />
+                        <span v-if="selectedSection">
+                            {{ selectedSection.name }}
+                        </span>
+                        <i v-else> Select a section to filter by </i>
                     </template>
 
-                    <BDropdownItem
-                        v-for="sec in defaultToolSections"
-                        :key="sec.id"
-                        :title="sec.description"
-                        :active="selectedSection?.id === sec.id"
-                        @click="applyQuotedFilter('section', sec.name)">
-                        <span v-localize>{{ sec.name }}</span>
-                    </BDropdownItem>
-                </BDropdownGroup>
-            </BDropdown>
+                    <BDropdownGroup
+                        id="searchable-sections"
+                        class="sections-select-list"
+                        header-classes="search-header">
+                        <template v-slot:header>
+                            <BDropdownText>
+                                <BFormInput
+                                    v-model="defaultToolSectionsFilter"
+                                    type="text"
+                                    placeholder="Filter sections..." />
+                            </BDropdownText>
+                        </template>
 
-            <GButton
-                v-if="selectedSection"
-                title="Remove section filter"
-                icon-only
-                inline
-                transparent
-                tooltip
-                @click="applyQuotedFilter('section', selectedSection.name)">
-                <FontAwesomeIcon :icon="faTimes" />
-            </GButton>
+                        <BDropdownItem
+                            v-for="sec in defaultToolSections"
+                            :key="sec.id"
+                            :title="sec.description"
+                            :active="selectedSection?.id === sec.id"
+                            @click="applyQuotedFilter('section', sec.name)">
+                            <span v-localize>{{ sec.name }}</span>
+                        </BDropdownItem>
+                    </BDropdownGroup>
+                </BDropdown>
 
-            <BDropdown
-                block
-                :disabled="props.disabled"
-                variant="link"
-                class="tool-section-dropdown"
-                toggle-class="text-decoration-none"
-                role="menu"
-                aria-label="Select a tool ontology to filter by"
-                size="sm">
-                <template v-slot:button-content>
-                    <span class="sr-only">Select a tool ontology to filter by</span>
-                    <FontAwesomeIcon :icon="faSitemap" />
-                    <span v-if="selectedOntology">
-                        {{ selectedOntology.name }}
-                    </span>
-                    <i v-else> Select an ontology to filter by </i>
-                </template>
+                <GButton
+                    v-if="selectedSection"
+                    title="Remove section filter"
+                    icon-only
+                    inline
+                    transparent
+                    tooltip
+                    @click="applyQuotedFilter('section', selectedSection.name)">
+                    <FontAwesomeIcon :icon="faTimes" />
+                </GButton>
 
-                <BDropdownGroup id="searchable-sections" class="sections-select-list" header-classes="search-header">
-                    <template v-slot:header>
-                        <BDropdownText>
-                            <BFormInput v-model="ontologiesFilter" type="text" placeholder="Filter ontologies..." />
-                        </BDropdownText>
+                <BDropdown
+                    block
+                    :disabled="props.disabled"
+                    variant="link"
+                    class="tool-section-dropdown"
+                    toggle-class="text-decoration-none"
+                    role="menu"
+                    aria-label="Select a tool ontology to filter by"
+                    size="sm">
+                    <template v-slot:button-content>
+                        <span class="sr-only">Select a tool ontology to filter by</span>
+                        <FontAwesomeIcon :icon="faSitemap" />
+                        <span v-if="selectedOntology">
+                            {{ selectedOntology.name }}
+                        </span>
+                        <i v-else> Select an ontology to filter by </i>
                     </template>
 
-                    <BDropdownGroup v-if="Object.keys(edamOperations).length" id="edam-operations" class="unselectable">
+                    <BDropdownGroup
+                        id="searchable-sections"
+                        class="sections-select-list"
+                        header-classes="search-header">
                         <template v-slot:header>
-                            <FontAwesomeIcon
-                                v-if="getPanelIcon('ontology:edam_operations')"
-                                :icon="getPanelIcon('ontology:edam_operations')"
-                                fixed-width
-                                size="sm" />
-                            <small class="font-weight-bold">{{ panels["ontology:edam_operations"]?.name }}</small>
+                            <BDropdownText>
+                                <BFormInput v-model="ontologiesFilter" type="text" placeholder="Filter ontologies..." />
+                            </BDropdownText>
                         </template>
-                        <BDropdownItem
-                            v-for="ont in edamOperations"
-                            :key="ont.id"
-                            :title="ont.description"
-                            :active="selectedOntology?.id === ont.id"
-                            @click="applyQuotedFilter('ontology', ont.id)">
-                            <span v-localize>{{ ont.name }}</span>
-                        </BDropdownItem>
+
+                        <BDropdownGroup
+                            v-if="Object.keys(edamOperations).length"
+                            id="edam-operations"
+                            class="unselectable">
+                            <template v-slot:header>
+                                <FontAwesomeIcon
+                                    v-if="getPanelIcon('ontology:edam_operations')"
+                                    :icon="getPanelIcon('ontology:edam_operations')"
+                                    fixed-width
+                                    size="sm" />
+                                <small class="font-weight-bold">{{ panels["ontology:edam_operations"]?.name }}</small>
+                            </template>
+                            <BDropdownItem
+                                v-for="ont in edamOperations"
+                                :key="ont.id"
+                                :title="ont.description"
+                                :active="selectedOntology?.id === ont.id"
+                                @click="applyQuotedFilter('ontology', ont.id)">
+                                <span v-localize>{{ ont.name }}</span>
+                            </BDropdownItem>
+                        </BDropdownGroup>
+
+                        <BDropdownDivider />
+
+                        <BDropdownGroup v-if="Object.keys(edamTopics).length" id="edam-topics" class="unselectable">
+                            <template v-slot:header>
+                                <FontAwesomeIcon
+                                    v-if="getPanelIcon('ontology:edam_topics')"
+                                    :icon="getPanelIcon('ontology:edam_topics')"
+                                    fixed-width
+                                    size="sm" />
+                                <small class="font-weight-bold">{{ panels["ontology:edam_topics"]?.name }}</small>
+                            </template>
+                            <BDropdownItem
+                                v-for="ont in edamTopics"
+                                :key="ont.id"
+                                :title="ont.description"
+                                :active="selectedOntology?.id === ont.id"
+                                @click="applyQuotedFilter('ontology', ont.id)">
+                                <span v-localize>{{ ont.name }}</span>
+                            </BDropdownItem>
+                        </BDropdownGroup>
                     </BDropdownGroup>
+                </BDropdown>
 
-                    <BDropdownDivider />
+                <GButton
+                    v-if="selectedOntology"
+                    title="Remove ontology filter"
+                    icon-only
+                    inline
+                    transparent
+                    tooltip
+                    @click="applyQuotedFilter('ontology', selectedOntology.id)">
+                    <FontAwesomeIcon :icon="faTimes" />
+                </GButton>
+            </div>
 
-                    <BDropdownGroup v-if="Object.keys(edamTopics).length" id="edam-topics" class="unselectable">
-                        <template v-slot:header>
-                            <FontAwesomeIcon
-                                v-if="getPanelIcon('ontology:edam_topics')"
-                                :icon="getPanelIcon('ontology:edam_topics')"
-                                fixed-width
-                                size="sm" />
-                            <small class="font-weight-bold">{{ panels["ontology:edam_topics"]?.name }}</small>
-                        </template>
-                        <BDropdownItem
-                            v-for="ont in edamTopics"
-                            :key="ont.id"
-                            :title="ont.description"
-                            :active="selectedOntology?.id === ont.id"
-                            @click="applyQuotedFilter('ontology', ont.id)">
-                            <span v-localize>{{ ont.name }}</span>
-                        </BDropdownItem>
-                    </BDropdownGroup>
-                </BDropdownGroup>
-            </BDropdown>
-
-            <GButton
-                v-if="selectedOntology"
-                title="Remove ontology filter"
-                icon-only
-                inline
-                transparent
-                tooltip
-                @click="applyQuotedFilter('ontology', selectedOntology.id)">
-                <FontAwesomeIcon :icon="faTimes" />
-            </GButton>
+            <slot name="list-view-controls" />
         </div>
 
         <ToolOntologyCard v-if="selectedOntology?.description" :ontology="selectedOntology" header />
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 430f6620d44..28edc09a79e 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -119,6 +119,7 @@ markupsafe==3.0.3
 mdurl==0.1.2
 mercurial==7.1.1
 mistune==3.0.2
+more-itertools==10.8.0
 mrcfile==1.5.4
 msal==1.34.0
 msgpack==1.1.2
diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index dd87dd33ae5..b4622ff09ef 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -1242,9 +1242,16 @@ class WorkflowContentsManager(UsesAnnotations):
         """Get workflow scheduling resource parameters for this user and workflow or None if not configured."""
         return self._resource_mapper_function(trans=trans, stored_workflow=stored, workflow=workflow)
 
-    def _workflow_to_dict_editor(self, trans, stored, workflow, tooltip=True, is_subworkflow=False):
+    def _workflow_to_dict_editor(
+        self,
+        trans,
+        stored: Optional[StoredWorkflow],
+        workflow: Workflow,
+        tooltip: bool = True,
+        is_subworkflow: bool = False,
+    ):
         # Pack workflow data into a dictionary and return
-        data = {}
+        data: dict[str, Any] = {}
         data["name"] = workflow.name
         data["steps"] = {}
         data["upgrade_messages"] = {}
@@ -1258,7 +1265,9 @@ class WorkflowContentsManager(UsesAnnotations):
         data["source_metadata"] = workflow.source_metadata
         data["annotation"] = self.get_item_annotation_str(trans.sa_session, trans.user, stored) or ""
         data["comments"] = [comment.to_dict() for comment in workflow.comments]
-        data["tags"] = stored.make_tag_string_list()
+        if stored:
+            # subworkflow may not have StoredWorkflow
+            data["tags"] = stored.make_tag_string_list()
 
         output_label_index = set()
         input_step_types = set(workflow.input_step_types)
diff --git a/lib/galaxy/model/dataset_collections/rule_target_column_specification.yml b/lib/galaxy/model/dataset_collections/rule_target_column_specification.yml
index ab4c4ff981d..8df4d656155 100644
--- a/lib/galaxy/model/dataset_collections/rule_target_column_specification.yml
+++ b/lib/galaxy/model/dataset_collections/rule_target_column_specification.yml
@@ -48,6 +48,10 @@
 - doc: "dbkey maps to the dbkey target type"
   column_header: "dbkey"
   maps_to: "dbkey"
+- doc: "build maps to the dbkey target type"
+  column_header: "build"
+  maps_to: "dbkey"
+
 
 - doc: "filetype maps to the file_type target type"
   column_header: "file type"
@@ -55,6 +59,9 @@
 - doc: "extension maps to the file_type target type"
   column_header: "extension"
   maps_to: "file_type"
+- doc: "Type maps to the file_type target type"
+  column_header: "Type"
+  maps_to: "file_type"
 
 - doc: "info maps to the info target type"
   column_header: "info"
diff --git a/lib/galaxy/model/dataset_collections/rule_target_columns.py b/lib/galaxy/model/dataset_collections/rule_target_columns.py
index ee731311e18..0737ae27555 100644
--- a/lib/galaxy/model/dataset_collections/rule_target_columns.py
+++ b/lib/galaxy/model/dataset_collections/rule_target_columns.py
@@ -23,9 +23,11 @@ COLUMN_TITLE_PREFIXES: dict[str, RuleBuilderMappingTargetKey] = {
     "genome": "dbkey",
     "dbkey": "dbkey",
     "genomebuild": "dbkey",
+    "build": "dbkey",
     "filetype": "file_type",
     "extension": "file_type",
     "fileextension": "file_type",
+    "type": "file_type",
     "info": "info",
     "tag": "tags",
     "grouptag": "group_tags",
diff --git a/lib/galaxy/model/dataset_collections/workbook_util.py b/lib/galaxy/model/dataset_collections/workbook_util.py
index ffa43770b96..e687dfa3183 100644
--- a/lib/galaxy/model/dataset_collections/workbook_util.py
+++ b/lib/galaxy/model/dataset_collections/workbook_util.py
@@ -235,17 +235,24 @@ def load_workbook_from_base64(content: str) -> ReadOnlyWorkbook:
     is_excel = file_like.read(4) == b"\x50\x4b\x03\x04"
     workbook: ReadOnlyWorkbook
     file_like.seek(0)
-    try:
-        if is_excel:
+    if is_excel:
+        try:
             workbook = ExcelReadOnlyWorkbook(load_workbook(file_like, data_only=True))
-        else:
+        except Exception as e:
+            extra_message = str(e)
+            raise RequestParameterInvalidException(
+                f"The provided content is not a valid Excel file (or at least not one Galaxy knows how to parse). Please check the content and try again. The underlying error was [{extra_message}]"
+            )
+    else:
+        try:
             tabular = decoded_content.decode("utf-8")
             file_like_as_utf8 = StringIO(tabular)
             workbook = CsvReaderReadOnlyWorkbook(file_like_as_utf8)
-    except Exception:
-        raise RequestParameterInvalidException(
-            "The provided content is not a valid Excel file. Please check the content and try again."
-        )
+        except Exception as e:
+            extra_message = str(e)
+            raise RequestParameterInvalidException(
+                f"The provided content is not a parsable as a valid CSV or TSV (or at least not one Galaxy knows how to parse). Please check the content and try again. The underlying error was [{extra_message}]"
+            )
     return workbook
 
 
diff --git a/lib/galaxy/model/store/ro_crate_utils.py b/lib/galaxy/model/store/ro_crate_utils.py
index 2d71f50ee13..a063bbc99f7 100644
--- a/lib/galaxy/model/store/ro_crate_utils.py
+++ b/lib/galaxy/model/store/ro_crate_utils.py
@@ -523,6 +523,12 @@ class WorkflowRunCrateProfileBuilder:
             )
         )
         crate.mainEntity.append_to("input", formal_param)
+
+        # Handle case where output_value is None (e.g., optional parameter not provided)
+        output_value = None
+        if step.output_value:
+            output_value = step.output_value.value
+
         return crate.add(
             ContextEntity(
                 crate,
@@ -530,7 +536,7 @@ class WorkflowRunCrateProfileBuilder:
                 properties={
                     "@type": "PropertyValue",
                     "name": f"{param_id}",
-                    "value": step.output_value.value,
+                    "value": output_value,
                     "exampleOfWork": {"@id": formal_param.id},
                 },
             )
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 77077ac81dc..43190a7109f 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2325,6 +2325,7 @@ class Tool(UsesDictVisibleKeys, ToolParameterBundle):
         preferred_object_store_id: Optional[str] = DEFAULT_PREFERRED_OBJECT_STORE_ID,
         credentials_context: Optional[CredentialsContext] = None,
         input_format: InputFormatT = "legacy",
+        tags: Optional[list[str]] = None,
     ):
         """
         Process incoming parameters for this tool from the dict `incoming`,
@@ -2358,7 +2359,6 @@ class Tool(UsesDictVisibleKeys, ToolParameterBundle):
 
         # Reserved global tags parameter. Applies to all tool outputs.
         # This may change in the future if per-output tags are introduced.
-        tags = incoming.get("__tags", [])
         if tags:
             tag_handler = trans.tag_handler
             for _, hda in execution_tracker.output_datasets:
@@ -4259,7 +4259,7 @@ class KeepSuccessDatasetsTool(FilterDatasetsTool):
 
 class FilterEmptyDatasetsTool(FilterDatasetsTool):
     tool_type = "filter_empty_datasets_collection"
-    require_dataset_ok = False
+    require_dataset_ok = True
 
     @staticmethod
     def element_is_valid(element: model.DatasetCollectionElement):
diff --git a/lib/galaxy/tools/execution_helpers.py b/lib/galaxy/tools/execution_helpers.py
index 0bdb98eff7d..a9691fc89ff 100644
--- a/lib/galaxy/tools/execution_helpers.py
+++ b/lib/galaxy/tools/execution_helpers.py
@@ -79,8 +79,8 @@ def on_text_for_numeric_ids(ids: Optional[list[int]], prefix: Optional[str] = No
     # and once as param_name1.
     groups = []
     unique_ids = sorted(set(ids))
-    for group in consecutive_groups(unique_ids):
-        group = list(group)
+    for group_it in consecutive_groups(unique_ids):
+        group = list(group_it)
         if len(group) == 1:
             groups.append(str(group[0]))
         elif len(group) == 2:
diff --git a/lib/galaxy/webapps/galaxy/services/tools.py b/lib/galaxy/webapps/galaxy/services/tools.py
index 8396ced129c..aab2a660bfb 100644
--- a/lib/galaxy/webapps/galaxy/services/tools.py
+++ b/lib/galaxy/webapps/galaxy/services/tools.py
@@ -341,6 +341,7 @@ class ToolsService(ServiceBase):
         input_format = cast(InputFormatT, input_format)  # https://github.com/python/mypy/issues/15106
         if "data_manager_mode" in payload:
             incoming["__data_manager_mode"] = payload["data_manager_mode"]
+        tags = payload.get("__tags")
         vars = tool.handle_input(
             trans,
             incoming,
@@ -349,6 +350,7 @@ class ToolsService(ServiceBase):
             input_format=input_format,
             preferred_object_store_id=preferred_object_store_id,
             credentials_context=CredentialsContext(root=credentials_context) if credentials_context else None,
+            tags=tags,
         )
 
         new_pja_flush = False
diff --git a/lib/galaxy_test/api/test_tool_output_tagging.py b/lib/galaxy_test/api/test_tool_output_tagging.py
index 228849e214a..206d16648b8 100644
--- a/lib/galaxy_test/api/test_tool_output_tagging.py
+++ b/lib/galaxy_test/api/test_tool_output_tagging.py
@@ -27,7 +27,6 @@ class TestToolOutputTaggingApi(ApiTestCase):
             "history_id": history_id,
             "inputs": {
                 "input1": {"values": [{"src": "hda", "id": hda["id"]}]},
-                "__tags": ["t1", "t2"],
             },
             "input_format": "21.01",
             "__tags": ["t1", "t2"],
@@ -54,7 +53,6 @@ class TestToolOutputTaggingApi(ApiTestCase):
                     "batch": True,
                     "values": [{"src": "hdca", "id": hdca["id"]}],
                 },
-                "__tags": ["m1", "m2"],
             },
             "input_format": "21.01",
             "__tags": ["m1", "m2"],
diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg
index a2be829a76e..9769ebdfbc8 100644
--- a/packages/app/setup.cfg
+++ b/packages/app/setup.cfg
@@ -60,6 +60,7 @@ install_requires =
     Markdown
     MarkupSafe
     mercurial>=6.8.2
+    more-itertools
     nodejs-wheel>=22,<23
     packaging
     paramiko!=2.9.0,!=2.9.1
diff --git a/pyproject.toml b/pyproject.toml
index 217d0baced7..573d0b6156d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -59,6 +59,7 @@ dependencies = [
     "MarkupSafe",
     "mercurial>=6.8.2",  # Python 3.13 support
     "mrcfile",
+    "more-itertools",
     "msal",
     "nodejs-wheel>=22,<23",
     "numpy>=1.26.0",  # Python 3.12 support
diff --git a/test/integration/test_workflow_tasks.py b/test/integration/test_workflow_tasks.py
index 864f06c29a0..7014845fff0 100644
--- a/test/integration/test_workflow_tasks.py
+++ b/test/integration/test_workflow_tasks.py
@@ -74,6 +74,54 @@ class TestWorkflowTasksIntegration(PosixFileSourceSetup, IntegrationTestCase, Us
             bco = json.load(f)
         self.workflow_populator.validate_biocompute_object(bco)
 
+    def test_export_ro_crate_with_optional_parameter_without_value(self):
+        """Test exporting invocation with optional text parameter that has no value.
+
+        This tests the fix for the bug where step.output_value is None for optional
+        parameters that weren't provided, which caused AttributeError when creating RO-Crate.
+        """
+        with self.dataset_populator.test_history() as history_id:
+            summary = self._run_workflow_with_optional_parameter_without_value(history_id)
+            invocation_id = summary.invocation_id
+
+            # Export to RO-Crate - this should succeed without AttributeError
+            ro_crate_path = self.workflow_populator.download_invocation_to_store(invocation_id, extension="rocrate.zip")
+
+            # Verify the RO-Crate was created successfully
+            with CompressedFile(ro_crate_path) as cf:
+                assert cf.file_type == "zip"
+
+    def _run_workflow_with_optional_parameter_without_value(self, history_id: str) -> RunJobsSummary:
+        """Run a workflow with an optional text parameter that is not provided."""
+        workflow = """
+class: GalaxyWorkflow
+inputs:
+  input_data:
+    type: data
+  optional_text_param:
+    type: text
+    optional: true
+steps:
+  cat_step:
+    tool_id: cat
+    in:
+      input1: input_data
+outputs:
+  output_data:
+    outputSource: cat_step/out_file1
+"""
+        test_data = """
+input_data:
+  value: 1.bed
+  type: File
+"""
+        summary = self.workflow_populator.run_workflow(
+            workflow,
+            test_data=test_data,
+            history_id=history_id,
+        )
+        return summary
+
     def _export_invocation_to_format(self, extension: str, to_uri: bool):
         with self.dataset_populator.test_history() as history_id:
             summary = self._run_workflow_with_runtime_data_column_parameter(history_id)
diff --git a/test/unit/data/dataset_collections/test_workbook_util.py b/test/unit/data/dataset_collections/test_workbook_util.py
index 5d58c0f06b4..7e0df29aad1 100644
--- a/test/unit/data/dataset_collections/test_workbook_util.py
+++ b/test/unit/data/dataset_collections/test_workbook_util.py
@@ -1,4 +1,10 @@
-from galaxy.model.dataset_collections.workbook_util import index_to_excel_column
+import base64
+
+from galaxy.model.dataset_collections.workbook_util import (
+    index_to_excel_column,
+    load_workbook_from_base64,
+)
+from galaxy.util.resources import resource_path
 
 
 def test_index_to_excel_column():
@@ -8,3 +14,18 @@ def test_index_to_excel_column():
     assert index_to_excel_column(700) == "ZY"
     assert index_to_excel_column(701) == "ZZ"
     assert index_to_excel_column(702) == "AAA"
+
+
+def test_load_workbook_from_base64():
+    workbook_base64 = resource_path_to_base64("filled_in_workbook_1.xlsx")
+    workbook = load_workbook_from_base64(workbook_base64)
+    assert workbook is not None
+
+    workbook_base64 = resource_path_to_base64("filled_in_workbook_1.tsv")
+    workbook = load_workbook_from_base64(workbook_base64)
+    assert workbook is not None
+
+
+def resource_path_to_base64(resource_name: str) -> str:
+    resource_bytes = resource_path("galaxy.model.unittest_utils", resource_name).read_bytes()
+    return base64.b64encode(resource_bytes).decode("utf-8")