diff --git a/client/src/api/tools.ts b/client/src/api/tools.ts
index 7ef06925577..16cd60c4591 100644
--- a/client/src/api/tools.ts
+++ b/client/src/api/tools.ts
@@ -1,5 +1,6 @@
 import { type components, GalaxyApi } from "@/api";
 import { ERROR_STATES, type ShowFullJobResponse } from "@/api/jobs";
+import type { Tool, ToolPanelItem, ToolSection, ToolSectionLabel } from "@/stores/toolStore";
 import { errorMessageAsString } from "@/utils/simple-error";
 
 export type HdcaUploadTarget = components["schemas"]["HdcaDataItemsTarget"];
@@ -130,3 +131,17 @@ export function fetchJobErrorMessage(jobDetails: ShowFullJobResponse): string |
     }
     return errorMessage;
 }
+
+// TODO: Once the backend models are typed, make sure these type guards are correct.
+export function isTool(section: ToolPanelItem): section is Tool {
+    return !isToolSection(section) && !isToolSectionLabel(section);
+}
+export function isToolSection(section: ToolPanelItem): section is ToolSection {
+    return (section as ToolSection).tools !== undefined || (section as ToolSection).elems !== undefined;
+}
+export function isToolSectionLabel(section: ToolPanelItem): section is ToolSectionLabel {
+    return (
+        (section as ToolSectionLabel).text !== undefined &&
+        (section as ToolSectionLabel).model_class === "ToolSectionLabel"
+    );
+}
diff --git a/client/src/components/Panels/Common/Tool.vue b/client/src/components/Panels/Common/Tool.vue
index 3e3a1b5553a..f47c2011af3 100644
--- a/client/src/components/Panels/Common/Tool.vue
+++ b/client/src/components/Panels/Common/Tool.vue
@@ -1,135 +1,96 @@
-<template>
-    <div class="toolTitle">
-        <a v-if="tool.disabled" :data-tool-id="tool.id" class="title-link name text-muted tool-link">
-            <span v-if="!hideName">{{ tool.name }}</span>
-            <span class="description">{{ tool.description }}</span>
-        </a>
-        <a
-            v-else
-            :class="targetClass"
-            :data-tool-id="tool.id"
-            :href="toolLink"
-            :target="toolTarget"
-            :title="tool.help"
-            @click="onClick">
-            <span class="labels">
-                <span
-                    v-for="(label, index) in tool.labels"
-                    :key="index"
-                    :class="['badge', 'badge-primary', `badge-${label}`]">
-                    {{ label }}
-                </span>
-            </span>
-            <span v-if="!hideName" class="name font-weight-bold">{{ tool.name }}</span>
-            <span class="description">{{ tool.description }}</span>
-            <span
-                v-b-tooltip.hover
-                :class="['operation', 'float-right', operationIcon]"
-                :title="operationTitle"
-                @click.stop.prevent="onOperation" />
-        </a>
-        <ToolFavoriteButton
-            v-if="showFavoriteAction"
-            :id="tool.id"
-            :class="['tool-favorite-button', { 'tool-favorite-button-hover': showFavoriteOnHover }]"
-            :data-tool-id="tool.id"
-            color="grey" />
-    </div>
-</template>
-
-<script>
-import BootstrapVue from "bootstrap-vue";
+<script setup lang="ts">
 import { storeToRefs } from "pinia";
-import Vue, { computed } from "vue";
+import { computed } from "vue";
 
+import type { Tool as ToolType } from "@/stores/toolStore";
 import { useToolStore } from "@/stores/toolStore";
 import { useUserStore } from "@/stores/userStore";
 import ariaAlert from "@/utils/ariaAlert";
 
 import ToolFavoriteButton from "@/components/Tool/Buttons/ToolFavoriteButton.vue";
 
-Vue.use(BootstrapVue);
+interface Props {
+    tool: ToolType;
+    operationTitle?: string;
+    operationIcon?: string;
+    hideName?: boolean;
+    showFavoriteButton?: boolean;
+}
 
-export default {
-    name: "Tool",
-    components: {
-        ToolFavoriteButton,
-    },
-    props: {
-        tool: {
-            type: Object,
-            required: true,
-        },
-        operationTitle: {
-            type: String,
-            default: "",
-        },
-        operationIcon: {
-            type: String,
-            default: "",
-        },
-        hideName: {
-            type: Boolean,
-            default: false,
-        },
-        toolKey: {
-            type: String,
-            default: "",
-        },
-        renderIcon: {
-            type: Boolean,
-            default: false,
-        },
-        showFavoriteButton: {
-            type: Boolean,
-            default: false,
-        },
-    },
-    setup(props) {
-        const toolStore = useToolStore();
-        const userStore = useUserStore();
-        const { currentFavorites } = storeToRefs(userStore);
-        const isFavorite = computed(() => currentFavorites.value.tools?.includes(props.tool.id));
-        return {
-            getLinkById: toolStore.getLinkById,
-            getTargetById: toolStore.getTargetById,
-            isFavorite,
-        };
-    },
-    computed: {
-        toolLink() {
-            return this.getLinkById(this.tool.id);
-        },
-        toolTarget() {
-            return this.getTargetById(this.tool.id);
-        },
-        targetClass() {
-            if (this.toolKey) {
-                return `tool-menu-item-${this.tool[this.toolKey]} title-link cursor-pointer tool-link`;
-            } else {
-                return `title-link cursor-pointer tool-link`;
-            }
-        },
-        showFavoriteAction() {
-            return this.showFavoriteButton || this.isFavorite;
-        },
-        showFavoriteOnHover() {
-            return this.isFavorite;
-        },
-    },
-    methods: {
-        onClick(evt) {
-            ariaAlert(`${this.tool.name} selected from panel`);
-            this.$emit("onClick", this.tool, evt);
-        },
-        onOperation(evt) {
-            ariaAlert(`${this.tool.name} operation selected from panel`);
-            this.$emit("onOperation", this.tool, evt);
-        },
-    },
-};
+const props = withDefaults(defineProps<Props>(), {
+    operationTitle: "",
+    operationIcon: "",
+    hideName: false,
+    showFavoriteButton: false,
+});
+
+const emit = defineEmits<{
+    (e: "onClick", tool: ToolType, evt: MouseEvent): void;
+    (e: "onOperation", tool: ToolType, evt: MouseEvent | KeyboardEvent): void;
+}>();
+
+const toolStore = useToolStore();
+const userStore = useUserStore();
+const { currentFavorites } = storeToRefs(userStore);
+
+const isFavorite = computed(() => currentFavorites.value.tools?.includes(props.tool.id));
+
+const toolLink = computed(() => toolStore.getLinkById(props.tool.id));
+const toolTarget = computed(() => toolStore.getTargetById(props.tool.id));
+
+function onClick(evt: MouseEvent) {
+    ariaAlert(`${props.tool.name} selected from panel`);
+    emit("onClick", props.tool, evt);
+}
+
+function onOperation(evt: MouseEvent | KeyboardEvent) {
+    ariaAlert(`${props.tool.name} operation selected from panel`);
+    emit("onOperation", props.tool, evt);
+}
 </script>
 
+<template>
+    <div class="toolTitle">
+        <a v-if="props.tool.disabled" :data-tool-id="props.tool.id" class="title-link name text-muted tool-link">
+            <span v-if="!props.hideName">{{ props.tool.name }}</span>
+            <span class="description">{{ props.tool.description }}</span>
+        </a>
+        <a
+            v-else
+            class="title-link cursor-pointer tool-link"
+            :data-tool-id="props.tool.id"
+            :href="toolLink"
+            :target="toolTarget"
+            :title="props.tool.help"
+            @click="onClick">
+            <span class="labels">
+                <span
+                    v-for="(label, index) in props.tool.labels"
+                    :key="index"
+                    :class="['badge', 'badge-primary', `badge-${label}`]">
+                    {{ label }}
+                </span>
+            </span>
+            <span v-if="!props.hideName" class="name font-weight-bold">{{ props.tool.name }}</span>
+            <span class="description">{{ props.tool.description }}</span>
+            <span
+                v-b-tooltip.hover
+                :class="['operation', 'float-right', props.operationIcon]"
+                role="button"
+                tabindex="0"
+                :title="props.operationTitle"
+                @keydown.enter.prevent="onOperation"
+                @click.stop.prevent="onOperation" />
+        </a>
+        <ToolFavoriteButton
+            v-if="props.showFavoriteButton || isFavorite"
+            :id="props.tool.id"
+            :class="['tool-favorite-button', { 'tool-favorite-button-hover': isFavorite }]"
+            :data-tool-id="props.tool.id"
+            color="grey" />
+    </div>
+</template>
+
 <style scoped>
 .toolTitle {
     display: flex;
diff --git a/client/src/components/Panels/Common/ToolPanelLabel.vue b/client/src/components/Panels/Common/ToolPanelLabel.vue
index 9474ec4958a..4246820fae0 100644
--- a/client/src/components/Panels/Common/ToolPanelLabel.vue
+++ b/client/src/components/Panels/Common/ToolPanelLabel.vue
@@ -88,7 +88,7 @@ function onKeydown(event: KeyboardEvent) {
                 @click.stop="clearRecentTools">
                 <FontAwesomeIcon :icon="faBroom" />
             </GButton>
-            <ToolPanelLinks :links="definition.links || undefined" />
+            <ToolPanelLinks v-if="definition.links" :links="definition.links" />
         </span>
     </div>
 </template>
diff --git a/client/src/components/Panels/Common/ToolPanelLinks.vue b/client/src/components/Panels/Common/ToolPanelLinks.vue
index 4c95bebea58..e48798e95e3 100644
--- a/client/src/components/Panels/Common/ToolPanelLinks.vue
+++ b/client/src/components/Panels/Common/ToolPanelLinks.vue
@@ -1,3 +1,18 @@
+<script setup lang="ts">
+import { faExternalLinkAlt } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { computed } from "vue";
+
+const props = defineProps<{
+    links: Record<string, string>;
+}>();
+
+const link = computed(() => {
+    const links = Object.values(props.links);
+    return links.length > 0 ? links[0] : null;
+});
+</script>
+
 <template>
     <span v-if="link" class="tool-panel-links">
         <a :href="link" target="_blank" style="display: inline">
@@ -6,29 +21,3 @@
         </a>
     </span>
 </template>
-
-<script>
-import { faExternalLinkAlt } from "@fortawesome/free-solid-svg-icons";
-import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-
-export default {
-    components: { FontAwesomeIcon },
-    props: {
-        links: {
-            type: Object,
-            default: () => ({}),
-        },
-    },
-    data() {
-        return {
-            faExternalLinkAlt,
-        };
-    },
-    computed: {
-        link() {
-            const links = Object.values(this.links || {});
-            return links.length > 0 ? links[0] : null;
-        },
-    },
-};
-</script>
diff --git a/client/src/components/Panels/Common/ToolSection.vue b/client/src/components/Panels/Common/ToolSection.vue
index f1e50170ac3..1a8b9a90613 100644
--- a/client/src/components/Panels/Common/ToolSection.vue
+++ b/client/src/components/Panels/Common/ToolSection.vue
@@ -4,8 +4,9 @@ import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { useEventBus } from "@vueuse/core";
 import { computed, onMounted, onUnmounted, ref, watch } from "vue";
 
+import { isTool, isToolSection, isToolSectionLabel } from "@/api/tools";
 import { useConfig } from "@/composables/config";
-import { type Tool as ToolType, type ToolSection, type ToolSectionLabel, useToolStore } from "@/stores/toolStore";
+import { type Tool as ToolType, type ToolPanelItem, useToolStore } from "@/stores/toolStore";
 import ariaAlert from "@/utils/ariaAlert";
 
 import Tool from "./Tool.vue";
@@ -13,7 +14,7 @@ import ToolPanelLabel from "./ToolPanelLabel.vue";
 import ToolPanelLinks from "./ToolPanelLinks.vue";
 
 const emit = defineEmits<{
-    (e: "onClick", tool: any, evt: Event): void;
+    (e: "onClick", tool: ToolType, evt: Event): void;
     (e: "onFilter", filter: string): void;
     (e: "onOperation", tool: any, evt: Event): void;
     (e: "onLabelToggle", labelId: string): void;
@@ -22,14 +23,12 @@ const emit = defineEmits<{
 const eventBus = useEventBus<string>("open-tool-section");
 
 interface Props {
-    category: ToolSection | ToolType | ToolSectionLabel;
+    category: ToolPanelItem;
     queryFilter?: string;
     disableFilter?: boolean;
     hideName?: boolean;
     operationTitle?: string;
     operationIcon?: string;
-    toolKey?: string;
-    sectionName?: string;
     expanded?: boolean;
     sortItems?: boolean;
     hasFilterButton?: boolean;
@@ -44,8 +43,6 @@ const props = withDefaults(defineProps<Props>(), {
     hideName: false,
     operationTitle: "",
     operationIcon: "",
-    toolKey: "",
-    sectionName: "default",
     expanded: false,
     sortItems: true,
     hasFilterButton: false,
@@ -57,38 +54,39 @@ const props = withDefaults(defineProps<Props>(), {
 const { config, isConfigLoaded } = useConfig();
 const toolStore = useToolStore();
 
+/**
+ * We can have sections of 2 types:
+ * 1. Sections with `elems` property, which is an array of tools and sections.
+ * 2. Sections with `tools` property, which is an array of tool IDs (strings) and section labels.
+ *    In this case, we need to resolve the tool IDs to get the actual tools.
+ */
 const elems = computed(() => {
-    if (toolSection.value.elems !== undefined && toolSection.value.elems.length > 0) {
-        return toolSection.value.elems.filter((el) => el !== null && el !== undefined);
-    }
-    if (toolSection.value.tools !== undefined && toolSection.value.tools.length > 0) {
-        return toolSection.value.tools
-            .map((toolId) => {
-                const tool = toolStore.getToolForId(toolId as string);
-                if (!tool && typeof toolId !== "string") {
-                    return toolId as ToolSectionLabel;
-                } else {
-                    return tool;
-                }
-            })
-            .filter((el) => el !== null && el !== undefined);
+    if (isToolSection(props.category)) {
+        if (props.category.elems !== undefined && props.category.elems.length > 0) {
+            // This section has `elems`, we can return it as is.
+            return props.category.elems;
+        }
+        if (props.category.tools !== undefined && props.category.tools.length > 0) {
+            return props.category.tools
+                .map((toolOrLabel) => {
+                    if (typeof toolOrLabel === "string") {
+                        // This is a tool ID, we need to resolve it to get the actual `Tool`.
+                        return toolStore.getToolForId(toolOrLabel) || null;
+                    } else {
+                        // This is a `ToolSectionLabel`, we can return it as is.
+                        return toolOrLabel;
+                    }
+                })
+                .filter((el) => el !== null);
+        }
     }
     return [];
 });
 
-const toolSection = computed(() => props.category as ToolSection);
-const toolSectionLabel = computed(() => props.category as ToolSectionLabel);
-
-const name = computed(() => toolSection.value.title || toolSection.value.name);
-const isSection = computed(() => toolSection.value.tools !== undefined || toolSection.value.elems !== undefined);
-const hasElements = computed(() => elems.value.length > 0);
-const title = computed(() => props.category.description || undefined);
-const links = computed(() => toolSection.value.links || {});
-
 const opened = ref(props.expanded || checkFilter());
 const sectionToggleIcon = computed(() => (opened.value ? faChevronDown : faChevronRight));
 
-const sortedElements = computed(() => {
+const sortedElements = computed<Array<[string, ToolPanelItem]>>(() => {
     // If this.config.sortTools is true, sort the tools alphabetically
     // When administrators have manually inserted labels we respect
     // the order set and hope for the best from the integrated
@@ -98,12 +96,12 @@ const sortedElements = computed(() => {
         isConfigLoaded.value &&
         config.value.toolbox_auto_sort === true &&
         props.sortItems === true &&
-        !elems.value.some((el) => (el as ToolSectionLabel).text !== undefined && (el as ToolSectionLabel).text !== "")
+        !elems.value.some((el) => isToolSectionLabel(el) && el.text !== "")
     ) {
         const elements = [...elems.value];
         const sorted = elements.sort((a, b) => {
-            const aNameLower = (a as ToolSection).name.toLowerCase();
-            const bNameLower = (b as ToolSection).name.toLowerCase();
+            const aNameLower = "name" in a ? a.name.toLowerCase() : "";
+            const bNameLower = "name" in b ? b.name.toLowerCase() : "";
             if (aNameLower > bNameLower) {
                 return 1;
             } else if (aNameLower < bNameLower) {
@@ -128,9 +126,9 @@ watch(
 watch(
     () => opened.value,
     (newVal: boolean, oldVal: boolean) => {
-        if (newVal !== oldVal) {
+        if (newVal !== oldVal && isToolSection(props.category)) {
             const currentState = newVal ? "opened" : "closed";
-            ariaAlert(`${name.value} tools menu ${currentState}`);
+            ariaAlert(`${props.category.name} tools menu ${currentState}`);
         }
     },
 );
@@ -144,14 +142,14 @@ onUnmounted(() => {
 });
 
 function openToolSection(sectionId: string) {
-    if (isSection.value && sectionId == props.category?.id) {
+    if (isToolSection(props.category) && sectionId == props.category?.id) {
         toggleMenu(true);
     }
 }
 function checkFilter() {
     return !props.disableFilter && !!props.queryFilter;
 }
-function onClick(tool: any, evt: Event) {
+function onClick(tool: ToolType, evt: Event) {
     emit("onClick", tool, evt);
 }
 function onOperation(tool: any, evt: Event) {
@@ -169,11 +167,11 @@ function getCollapsedState(id: string): boolean | undefined {
 </script>
 
 <template>
-    <div v-if="isSection && hasElements" class="tool-panel-section">
+    <div v-if="isToolSection(props.category) && elems.length > 0" class="tool-panel-section">
         <div
             v-b-tooltip.topright.hover.noninteractive
-            :class="['toolSectionTitle', `tool-menu-section-${sectionName}`, 'tool-panel-divider']"
-            :title="title">
+            class="toolSectionTitle tool-panel-divider"
+            :title="props.category.description || undefined">
             <a
                 class="title-link tool-panel-divider-link"
                 href="javascript:void(0)"
@@ -183,15 +181,15 @@ function getCollapsedState(id: string): boolean | undefined {
                 <span class="tool-panel-divider-text">
                     <FontAwesomeIcon :icon="sectionToggleIcon" class="tool-panel-divider-toggle" />
                     <span class="name">
-                        {{ name }}
+                        {{ props.category.title || props.category.name }}
                     </span>
-                    <ToolPanelLinks :links="links" />
+                    <ToolPanelLinks v-if="props.category.links" :links="props.category.links" />
                     <button
-                        v-if="isSection && props.hasFilterButton"
+                        v-if="props.hasFilterButton"
                         v-b-tooltip.hover.noninteractive.bottom
                         title="Show full section"
                         class="inline-icon-button"
-                        @click.stop="emit('onFilter', `section:${toolSection.name}`)">
+                        @click.stop="emit('onFilter', `section:${props.category.name}`)">
                         <FontAwesomeIcon :icon="faFilter" />
                     </button>
                 </span>
@@ -201,17 +199,16 @@ function getCollapsedState(id: string): boolean | undefined {
             <div v-if="opened" data-description="opened tool panel section">
                 <template v-for="[key, el] in sortedElements">
                     <ToolPanelLabel
-                        v-if="toolSectionLabel.text || el.model_class === 'ToolSectionLabel'"
+                        v-if="isToolSectionLabel(el)"
                         :key="`label-${key}`"
                         :definition="el"
                         :collapsed="getCollapsedState(el.id)"
                         @toggle="onLabelToggle" />
                     <Tool
-                        v-else
+                        v-else-if="isTool(el)"
                         :key="`tool-${key}`"
                         class="ml-2"
                         :tool="el"
-                        :tool-key="toolKey"
                         :hide-name="hideName"
                         :operation-title="operationTitle"
                         :operation-icon="operationIcon"
@@ -222,22 +219,20 @@ function getCollapsedState(id: string): boolean | undefined {
             </div>
         </transition>
     </div>
-    <div v-else>
-        <ToolPanelLabel
-            v-if="toolSectionLabel.text"
-            :definition="toolSectionLabel"
-            :collapsed="getCollapsedState(toolSectionLabel.id)"
-            @toggle="onLabelToggle" />
-        <Tool
-            v-else
-            :tool="category"
-            :hide-name="hideName"
-            :operation-title="operationTitle"
-            :operation-icon="operationIcon"
-            :show-favorite-button="props.showFavoriteButton || searchActive"
-            @onOperation="onOperation"
-            @onClick="onClick" />
-    </div>
+    <ToolPanelLabel
+        v-else-if="isToolSectionLabel(props.category)"
+        :definition="props.category"
+        :collapsed="getCollapsedState(props.category.id)"
+        @toggle="onLabelToggle" />
+    <Tool
+        v-else-if="isTool(props.category)"
+        :tool="props.category"
+        :hide-name="hideName"
+        :operation-title="operationTitle"
+        :operation-icon="operationIcon"
+        :show-favorite-button="props.showFavoriteButton || searchActive"
+        @onOperation="onOperation"
+        @onClick="onClick" />
 </template>
 
 <style lang="scss" scoped>
diff --git a/client/src/components/Panels/ToolBox.vue b/client/src/components/Panels/ToolBox.vue
index b170a0db8cf..6d0c3e77a63 100644
--- a/client/src/components/Panels/ToolBox.vue
+++ b/client/src/components/Panels/ToolBox.vue
@@ -8,7 +8,7 @@ import { computed, type ComputedRef, type Ref, ref, watch } from "vue";
 import { useGlobalUploadModal } from "@/composables/globalUploadModal";
 import { useToolRouting } from "@/composables/route";
 import { useFavoriteSearchResults, useToolPanelFavorites } from "@/composables/toolPanelFavorites";
-import type { Tool, ToolSection as ToolSectionType, ToolSectionLabel } from "@/stores/toolStore";
+import type { Tool, ToolPanelItem, ToolSection as ToolSectionType } from "@/stores/toolStore";
 import { useToolStore } from "@/stores/toolStore";
 import { useUserStore } from "@/stores/userStore";
 import localize from "@/utils/localization";
@@ -132,8 +132,6 @@ const localSectionsById = computed(() => {
     ) as Record<string, Tool | ToolSectionType>;
 });
 
-type PanelItem = Tool | ToolSectionType | ToolSectionLabel;
-
 // Use composable for favorites and recent tools management
 const {
     favoritesCollapsed,
@@ -189,14 +187,14 @@ const searchPanelSections = computed(() => {
 
 const toolsList = computed(() => Object.values(localToolsById.value));
 
-const flatResultsPanel = computed<Record<string, PanelItem> | null>(() => {
+const flatResultsPanel = computed<Record<string, ToolPanelItem> | null>(() => {
     if (!hasResults.value) {
         return null;
     }
     if (!hasMixedResults.value) {
-        return filterTools(localToolsById.value, results.value) as Record<string, PanelItem>;
+        return filterTools(localToolsById.value, results.value) as Record<string, ToolPanelItem>;
     }
-    const entries: Array<[string, PanelItem]> = [];
+    const entries: Array<[string, ToolPanelItem]> = [];
     entries.push([
         PANEL_LABEL_IDS.FAVORITES_RESULTS_LABEL,
         buildToolLabel(PANEL_LABEL_IDS.FAVORITES_RESULTS_LABEL, localize("Favorites")),
@@ -212,11 +210,11 @@ const flatResultsPanel = computed<Record<string, PanelItem> | null>(() => {
     return Object.fromEntries(entries);
 });
 
-const favoritesDefaultPanel = computed<Record<string, PanelItem> | null>(() => {
+const favoritesDefaultPanel = computed<Record<string, ToolPanelItem> | null>(() => {
     if (!props.favoritesDefault || query.value) {
         return null;
     }
-    const entries: Array<[string, PanelItem]> = [];
+    const entries: Array<[string, ToolPanelItem]> = [];
     const favorites = favoriteToolIdsInPanel.value;
     const recents = recentToolIdsToShow.value;
 
@@ -278,7 +276,7 @@ const sectionedResultsPanel = computed<Record<string, Tool | ToolSectionType> |
  * If we have results for search, we show tools in sections or just tools,
  * based on whether `showSections` is true or false
  */
-const localPanel: ComputedRef<Record<string, PanelItem> | null> = computed(() => {
+const localPanel: ComputedRef<Record<string, ToolPanelItem> | null> = computed(() => {
     if (props.favoritesDefault && !query.value) {
         return favoritesDefaultPanel.value || {};
     }
diff --git a/client/src/components/Panels/utilities.test.ts b/client/src/components/Panels/utilities.test.ts
index 0784b604182..6adade4bcd5 100644
--- a/client/src/components/Panels/utilities.test.ts
+++ b/client/src/components/Panels/utilities.test.ts
@@ -36,7 +36,7 @@ const tempToolPanel = {
             id: "fasta/fastq",
             name: "FASTA/FASTQ",
         },
-    },
+    } as unknown as Record<string, ToolSection>,
 };
 const tempToolsList = {
     tools: {
diff --git a/client/src/components/Panels/utilities.ts b/client/src/components/Panels/utilities.ts
index f9d1fd470e1..55121523833 100644
--- a/client/src/components/Panels/utilities.ts
+++ b/client/src/components/Panels/utilities.ts
@@ -14,6 +14,7 @@ import {
 } from "@fortawesome/free-solid-svg-icons";
 import { orderBy } from "lodash";
 
+import { isTool, isToolSection } from "@/api/tools";
 import type { FilterSettings as ToolFilters, Tool, ToolSection, ToolSectionLabel } from "@/stores/toolStore";
 import levenshteinDistance from "@/utils/levenshtein";
 
@@ -71,7 +72,7 @@ const FILTER_KEYS = {
 const STRING_REPLACEMENTS: string[] = [" ", "-", "\\(", "\\)", "'", ":", `"`];
 const MINIMUM_DL_LENGTH = 5; // for Demerau-Levenshtein distance
 const MINIMUM_WORD_MATCH = 2; // for word match
-const UNSECTIONED_SECTION = {
+const UNSECTIONED_SECTION: ToolSection = {
     // to return a section for unsectioned tools
     model_class: "ToolSection",
     id: "unsectioned",
@@ -243,25 +244,28 @@ export function getValidToolsInCurrentView(
 export function getValidToolsInEachSection(
     validToolIdsInCurrentView: string[],
     currentPanel: Record<string, Tool | ToolSection>,
-) {
+): Array<[string, Tool | ToolSection]> {
     // use a set for fast membership lookup
     const idSet = new Set(validToolIdsInCurrentView);
     return Object.entries(currentPanel).map(([id, section]) => {
-        const validatedSection = { ...section } as ToolSection;
-        // assign sectionTools to avoid repeated getter access
-        const sectionTools = validatedSection.tools;
-        if (sectionTools && Array.isArray(sectionTools)) {
-            // filter on valid tools and panel labels in this section
-            validatedSection.tools = sectionTools.filter((toolId) => {
-                if (typeof toolId === "string" && idSet.has(toolId)) {
-                    return true;
-                } else if (typeof toolId !== "string") {
-                    // is a special case where there is a label within a section
-                    return true;
-                }
-            });
+        if (isToolSection(section)) {
+            const validatedSection = { ...section };
+            // assign sectionTools to avoid repeated getter access
+            const sectionTools = validatedSection.tools;
+            if (sectionTools && Array.isArray(sectionTools)) {
+                // filter on valid tools and panel labels in this section
+                validatedSection.tools = sectionTools.filter((toolId) => {
+                    if (typeof toolId === "string" && idSet.has(toolId)) {
+                        return true;
+                    } else if (typeof toolId !== "string") {
+                        // is a special case where there is a label within a section
+                        return true;
+                    }
+                });
+            }
+            return [id, validatedSection];
         }
-        return [id, validatedSection];
+        return [id, section];
     });
 }
 
@@ -272,20 +276,18 @@ export function getValidToolsInEachSection(
  * @returns a `currentPanel` object containing sections/tools/labels that meet required conditions
  */
 export function getValidPanelItems(
-    items: (string | ToolSection)[][],
+    items: Array<[string, ToolSection | Tool]>,
     validToolIdsInCurrentView: string[],
     excludedSectionIds: string[] = [],
 ) {
     const validEntries = items.filter(([id, item]) => {
-        id = id as string;
-        item = item as Tool | ToolSection;
-        if (isToolObject(item as Tool) && validToolIdsInCurrentView.includes(id)) {
+        if (isTool(item) && validToolIdsInCurrentView.includes(id)) {
             // is a `Tool` and is in `localToolsById`
             return true;
-        } else if (item.tools === undefined) {
+        } else if (!isToolSection(item)) {
             // is neither a `Tool` nor a `ToolSection`, maybe a `ToolSectionLabel`
             return true;
-        } else if (item.tools && item.tools.length > 0 && !excludedSectionIds.includes(id)) {
+        } else if ("tools" in item && item.tools?.length && !excludedSectionIds.includes(id)) {
             // is a `ToolSection` with tools; is not an excluded section
             return true;
         } else {
@@ -483,12 +485,9 @@ export function createSortedResultPanel(matchedTools: SearchMatch[], currentPane
             const sections = Object.keys(currentPanel);
             for (const section of sections) {
                 let toolAdded = false;
-                const existingPanelItem = section ? currentPanel[section] : undefined;
-                if (existingPanelItem && section) {
-                    if (
-                        (existingPanelItem as ToolSection).tools &&
-                        (existingPanelItem as ToolSection).tools?.includes(match.id)
-                    ) {
+                const existingPanelItem = currentPanel[section];
+                if (existingPanelItem) {
+                    if ("tools" in existingPanelItem && existingPanelItem.tools?.includes(match.id)) {
                         // it has tools so is a section, and it has the tool we're looking for
 
                         // if we haven't seen this section yet, create it in the resultPanel
@@ -500,7 +499,7 @@ export function createSortedResultPanel(matchedTools: SearchMatch[], currentPane
                         existingSection.tools?.push(match.id);
                         acc[section] = existingSection;
                         toolAdded = true;
-                    } else if (isToolObject(existingPanelItem as Tool) && existingPanelItem.id === match.id) {
+                    } else if (isTool(existingPanelItem) && existingPanelItem.id === match.id) {
                         // it is a tool, and it is the tool we're looking for
 
                         // put in it the "Unsectioned Tools" section (if it doesn't exist, create it)
@@ -563,21 +562,6 @@ function closestSubstring(query: string, actualStr: string) {
     return null;
 }
 
-export function isToolObject(tool: Tool | ToolSection | ToolSectionLabel) {
-    // toolbox overhaul with typing will simplify this dramatically...
-    // Right now, our shorthand is that tools have no 'text', and don't match
-    // the model_class of the section/label.
-    if (
-        !(tool as ToolSectionLabel).text &&
-        tool.model_class !== "ToolSectionLabel" &&
-        tool.model_class !== "ToolSection" &&
-        (tool as ToolSection).tools === undefined
-    ) {
-        return true;
-    }
-    return false;
-}
-
 // given array and a substring, get the closest matching term for substring
 function matchingTerm(termArray: string[], substring: string) {
     const sanitized = sanitizeString(substring);
diff --git a/client/src/stores/toolStore.ts b/client/src/stores/toolStore.ts
index e4a922d39b3..77a5d78484c 100644
--- a/client/src/stores/toolStore.ts
+++ b/client/src/stores/toolStore.ts
@@ -37,6 +37,7 @@ export interface Panel {
     searchable: boolean;
 }
 
+// TODO: Once the backend models are typed, we will replace these with the generated types from the schema.
 export interface Tool {
     model_class: string;
     id: string;
@@ -64,10 +65,11 @@ export interface Tool {
         changeset_revision: string;
         tool_shed: string;
     };
+    help?: string;
 }
 
 export interface ToolSection {
-    model_class: string;
+    model_class: "ToolSection";
     id: string;
     name: string;
     title?: string;
@@ -75,11 +77,11 @@ export interface ToolSection {
     description?: string;
     links?: Record<string, string>;
     tools?: (string | ToolSectionLabel)[];
-    elems?: (Tool | ToolSection)[];
+    elems?: (Tool | ToolSection)[]; // TODO: Are we sure that a `ToolSection` can have `ToolSection` children?
 }
 
 export interface ToolSectionLabel {
-    model_class: string;
+    model_class: "ToolSectionLabel";
     id: string;
     text: string;
     version?: string;
@@ -87,6 +89,8 @@ export interface ToolSectionLabel {
     links?: Record<string, string> | null;
 }
 
+export type ToolPanelItem = Tool | ToolSection | ToolSectionLabel;
+
 export type ToolHelpData = {
     help?: string;
     summary?: string;
diff --git a/client/src/utils/navigation/navigation.yml b/client/src/utils/navigation/navigation.yml
index 21513da2270..37a88ab1154 100644
--- a/client/src/utils/navigation/navigation.yml
+++ b/client/src/utils/navigation/navigation.yml
@@ -939,8 +939,6 @@ workflow_editor:
       selector: 'license save'
       type: data-description
     tool_menu: '.toolMenuContainer'
-    tool_menu_section_link: '.tool-menu-section-${section_name} a span'
-    tool_menu_item_link: 'a.tool-menu-item-${item_name}'
     workflow_link:
       type: xpath
       selector: '//a[contains(., "${workflow_title}")]'
diff --git a/client/src/utils/navigation/schema.ts b/client/src/utils/navigation/schema.ts
index b85193eb3f9..cb59d30d7e5 100644
--- a/client/src/utils/navigation/schema.ts
+++ b/client/src/utils/navigation/schema.ts
@@ -447,8 +447,6 @@ interface Rootworkflow_editor extends Component {
     edit_annotation: SelectorTemplate;
     edit_name: SelectorTemplate;
     tool_menu: SelectorTemplate;
-    tool_menu_section_link: SelectorTemplate;
-    tool_menu_item_link: SelectorTemplate;
     workflow_link: SelectorTemplate;
     insert_steps: SelectorTemplate;
     connect_icon: SelectorTemplate;