diff --git a/client/src/components/Collections/ListCollectionCreator.vue b/client/src/components/Collections/ListCollectionCreator.vue
index ca9e25aec41..d33f98927d8 100644
--- a/client/src/components/Collections/ListCollectionCreator.vue
+++ b/client/src/components/Collections/ListCollectionCreator.vue
@@ -414,6 +414,7 @@ function renameElement(element: any, name: string) {
                 :extensions="extensions"
                 collection-type="list"
                 :no-items="props.initialElements.length == 0 && !props.fromSelection"
+                :show-upload="!fromSelection"
                 @add-uploaded-files="addUploadedFiles"
                 @on-update-datatype-toggle="changeDatatypeFilter"
                 @onUpdateHideSourceItems="onUpdateHideSourceItems"
diff --git a/client/src/components/Collections/PairCollectionCreator.vue b/client/src/components/Collections/PairCollectionCreator.vue
index 1d3e5922f31..c00c2c0f9b1 100644
--- a/client/src/components/Collections/PairCollectionCreator.vue
+++ b/client/src/components/Collections/PairCollectionCreator.vue
@@ -376,6 +376,7 @@ function _naiveStartingAndEndingLCS(s1: string, s2: string) {
                 :extensions-toggle="removeExtensions"
                 collection-type="paired"
                 :no-items="props.initialElements.length == 0 && !props.fromSelection"
+                :show-upload="!fromSelection"
                 @add-uploaded-files="addUploadedFiles"
                 @onUpdateHideSourceItems="onUpdateHideSourceItems"
                 @clicked-create="clickedCreate"
diff --git a/client/src/components/Collections/PairedListCollectionCreator.vue b/client/src/components/Collections/PairedListCollectionCreator.vue
index 620252f7c28..1f831e66a79 100644
--- a/client/src/components/Collections/PairedListCollectionCreator.vue
+++ b/client/src/components/Collections/PairedListCollectionCreator.vue
@@ -881,6 +881,7 @@ function _naiveStartingAndEndingLCS(s1: string, s2: string) {
                 :extensions="extensions"
                 collection-type="list:paired"
                 :no-items="props.initialElements.length == 0 && !props.fromSelection"
+                :show-upload="!fromSelection"
                 @add-uploaded-files="addUploadedFiles"
                 @onUpdateHideSourceItems="hideSourceItems = $event"
                 @clicked-create="clickedCreate"
diff --git a/client/src/components/Collections/common/CollectionCreator.vue b/client/src/components/Collections/common/CollectionCreator.vue
index c60e80099fd..6947a1d592f 100644
--- a/client/src/components/Collections/common/CollectionCreator.vue
+++ b/client/src/components/Collections/common/CollectionCreator.vue
@@ -1,7 +1,7 @@
 <script setup lang="ts">
-import { faChevronDown, faChevronUp, faPlus, faUpload } from "@fortawesome/free-solid-svg-icons";
+import { faPlus, faUpload } from "@fortawesome/free-solid-svg-icons";
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
-import { BAlert, BButton, BFormCheckbox, BFormGroup, BFormInput, BLink, BTab, BTabs } from "bootstrap-vue";
+import { BAlert, BTab, BTabs } from "bootstrap-vue";
 import { storeToRefs } from "pinia";
 import { computed, ref, watch } from "vue";
 
@@ -13,6 +13,12 @@ import { useUserStore } from "@/stores/userStore";
 import localize from "@/utils/localization";
 import { orList } from "@/utils/strings";
 
+import CollectionCreatorFooterButtons from "./CollectionCreatorFooterButtons.vue";
+import CollectionCreatorHelpHeader from "./CollectionCreatorHelpHeader.vue";
+import CollectionCreatorNoItemsMessage from "./CollectionCreatorNoItemsMessage.vue";
+import CollectionCreatorShowExtensions from "./CollectionCreatorShowExtensions.vue";
+import CollectionCreatorSourceOptions from "./CollectionCreatorSourceOptions.vue";
+import CollectionNameInput from "./CollectionNameInput.vue";
 import HelpText from "@/components/Help/HelpText.vue";
 import DefaultBox from "@/components/Upload/DefaultBox.vue";
 
@@ -40,12 +46,14 @@ interface Props {
     extensionsToggle?: boolean;
     noItems?: boolean;
     collectionType?: string;
+    showUpload: boolean;
 }
 
 const props = withDefaults(defineProps<Props>(), {
     suggestedName: "",
     extensions: undefined,
     extensionsToggle: false,
+    showUpload: true,
 });
 
 const emit = defineEmits<{
@@ -56,7 +64,6 @@ const emit = defineEmits<{
     (e: "add-uploaded-files", value: HDASummary[]): void;
 }>();
 
-const isExpanded = ref(false);
 const currentTab = ref(Tabs.create);
 const collectionName = ref(props.suggestedName);
 const localHideSourceItems = ref(props.hideSourceItems);
@@ -122,15 +129,14 @@ function addUploadedFiles(value: HDASummary[]) {
     emit("add-uploaded-files", value);
 }
 
-function clickForHelp() {
-    isExpanded.value = !isExpanded.value;
-    return isExpanded.value;
-}
-
 function cancelCreate() {
     props.oncancel();
 }
 
+function removeExtensionsToggle() {
+    emit("remove-extensions-toggle");
+}
+
 async function loadExtensions() {
     listExtensions.value = await getUploadDatatypes(false, AUTO_EXTENSION);
     extensionsSet.value = true;
@@ -147,51 +153,15 @@ watch(
 </script>
 
 <template>
-    <BTabs v-model="currentTab" fill justified>
-        <BTab class="collection-creator" :title="localize('Create Collection')">
+    <span>
+        <span v-if="!showUpload" class="collection-creator">
             <div v-if="props.noItems">
-                <BAlert variant="info" show>
-                    {{ localize("No items available to create a collection.") }}
-                    {{ localize("Exit and change your current history, or") }}
-                    <BLink class="text-decoration-none" @click.stop.prevent="currentTab = Tabs.upload">
-                        {{ localize("Upload some datasets.") }}
-                    </BLink>
-                </BAlert>
+                <CollectionCreatorNoItemsMessage @click-upload="currentTab = Tabs.upload" />
             </div>
             <div v-else>
-                <div class="header flex-row no-flex">
-                    <div class="main-help well clear" :class="{ expanded: isExpanded }">
-                        <a
-                            class="more-help"
-                            href="javascript:void(0);"
-                            role="button"
-                            :title="localize('Expand or Close Help')"
-                            @click="clickForHelp">
-                            <div v-if="!isExpanded">
-                                <FontAwesomeIcon :icon="faChevronDown" />
-                                <span class="sr-only">{{ localize("Expand Help") }}</span>
-                            </div>
-                            <div v-else>
-                                <FontAwesomeIcon :icon="faChevronUp" />
-                                <span class="sr-only">{{ localize("Close Help") }}</span>
-                            </div>
-                        </a>
-
-                        <div class="help-content">
-                            <!-- each collection that extends this will add their own help content -->
-                            <slot name="help-content"></slot>
-
-                            <a
-                                class="more-help"
-                                href="javascript:void(0);"
-                                role="button"
-                                :title="localize('Expand or Close Help')"
-                                @click="clickForHelp">
-                                <span class="sr-only">{{ localize("Expand Help") }}</span>
-                            </a>
-                        </div>
-                    </div>
-                </div>
+                <CollectionCreatorHelpHeader>
+                    <slot name="help-content"></slot>
+                </CollectionCreatorHelpHeader>
 
                 <div class="middle flex-row flex-row-container">
                     <slot name="middle-content"></slot>
@@ -199,105 +169,103 @@ watch(
 
                 <div class="footer flex-row">
                     <div class="vertically-spaced">
+                        <CollectionCreatorShowExtensions :extensions="extensions" />
+
                         <div class="d-flex align-items-center justify-content-between">
+                            <CollectionCreatorSourceOptions
+                                v-model="localHideSourceItems"
+                                :render-extensions-toggle="renderExtensionsToggle"
+                                :extensions-toggle="extensionsToggle"
+                                @remove-extensions-toggle="removeExtensionsToggle" />
+                            <CollectionNameInput
+                                v-model="collectionName"
+                                :short-what-is-being-created="shortWhatIsBeingCreated" />
+                        </div>
+                    </div>
+
+                    <CollectionCreatorFooterButtons
+                        :short-what-is-being-created="shortWhatIsBeingCreated"
+                        :valid-input="validInput"
+                        @clicked-cancel="cancelCreate"
+                        @clicked-create="emit('clicked-create', collectionName)" />
+                </div>
+            </div>
+        </span>
+        <BTabs v-else v-model="currentTab" fill justified>
+            <BTab class="collection-creator" :title="localize('Create Collection')">
+                <div v-if="props.noItems">
+                    <CollectionCreatorNoItemsMessage @click-upload="currentTab = Tabs.upload" />
+                </div>
+                <div v-else>
+                    <CollectionCreatorHelpHeader>
+                        <slot name="help-content"></slot>
+                    </CollectionCreatorHelpHeader>
+
+                    <div class="middle flex-row flex-row-container">
+                        <slot name="middle-content"></slot>
+                    </div>
+
+                    <div class="footer flex-row">
+                        <div class="vertically-spaced">
+                            <CollectionCreatorShowExtensions :extensions="extensions" />
+
+                            <div class="d-flex align-items-center justify-content-between">
+                                <CollectionCreatorSourceOptions
+                                    v-model="localHideSourceItems"
+                                    :render-extensions-toggle="renderExtensionsToggle"
+                                    :extensions-toggle="extensionsToggle" />
+                                <CollectionNameInput
+                                    v-model="collectionName"
+                                    :short-what-is-being-created="shortWhatIsBeingCreated" />
+                            </div>
+                        </div>
+
+                        <CollectionCreatorFooterButtons
+                            :short-what-is-being-created="shortWhatIsBeingCreated"
+                            :valid-input="validInput"
+                            @clicked-cancel="cancelCreate"
+                            @clicked-create="emit('clicked-create', collectionName)" />
+                    </div>
+                </div>
+            </BTab>
+            <BTab>
+                <template v-slot:title>
+                    <FontAwesomeIcon :icon="faUpload" fixed-width />
+                    <span>{{ localize("Upload Files to Add to Collection") }}</span>
+                </template>
+                <DefaultBox
+                    v-if="configOptions && extensionsSet"
+                    :chunk-upload-size="configOptions.chunkUploadSize"
+                    :default-db-key="configOptions.defaultDbKey"
+                    :default-extension="defaultExtension"
+                    :effective-extensions="props.extensions?.length ? validExtensions : listExtensions"
+                    :file-sources-configured="configOptions.fileSourcesConfigured"
+                    :ftp-upload-site="ftpUploadSite"
+                    :has-callback="false"
+                    :history-id="historyId"
+                    :list-db-keys="[]"
+                    disable-footer
+                    emit-uploaded
+                    @uploaded="addUploadedFiles"
+                    @dismiss="currentTab = Tabs.create">
+                    <template v-slot:footer>
+                        <div class="d-flex align-items-center justify-content-between mt-2">
                             <BAlert v-if="extensions?.length" class="w-100 py-0" variant="secondary" show>
                                 <HelpText
-                                    uri="galaxy.collections.collectionBuilder.filteredExtensions"
-                                    :text="localize('Filtered extensions: ')" />
+                                    uri="galaxy.collections.collectionBuilder.requiredUploadExtensions"
+                                    :text="localize('Required extensions: ')" />
                                 <strong>{{ orList(extensions) }}</strong>
                             </BAlert>
                         </div>
-
-                        <div class="d-flex align-items-center justify-content-between">
-                            <BFormGroup class="inputs-form-group">
-                                <BFormCheckbox
-                                    v-if="renderExtensionsToggle"
-                                    name="remove-extensions"
-                                    switch
-                                    :checked="extensionsToggle"
-                                    @input="emit('remove-extensions-toggle')">
-                                    {{ localize("Remove file extensions?") }}
-                                </BFormCheckbox>
-
-                                <div data-description="hide original elements">
-                                    <BFormCheckbox v-model="localHideSourceItems" name="hide-originals" switch>
-                                        <HelpText
-                                            uri="galaxy.collections.collectionBuilder.hideOriginalElements"
-                                            :text="localize('Hide original elements')" />
-                                    </BFormCheckbox>
-                                </div>
-                            </BFormGroup>
-
-                            <BFormGroup
-                                class="flex-gapx-1 d-flex align-items-center w-50 inputs-form-group"
-                                :label="localize('Name:')"
-                                label-for="collection-name">
-                                <BFormInput
-                                    id="collection-name"
-                                    v-model="collectionName"
-                                    class="collection-name"
-                                    :placeholder="localize('Enter a name for your new ' + shortWhatIsBeingCreated)"
-                                    size="sm"
-                                    required
-                                    :state="!collectionName ? false : null" />
-                            </BFormGroup>
-                        </div>
-                    </div>
-
-                    <div class="actions vertically-spaced d-flex justify-content-between">
-                        <BButton tabindex="-1" @click="cancelCreate">
-                            {{ localize("Cancel") }}
-                        </BButton>
-
-                        <BButton
-                            class="create-collection"
-                            variant="primary"
-                            :disabled="!validInput"
-                            @click="emit('clicked-create', collectionName)">
-                            {{ localize("Create " + shortWhatIsBeingCreated) }}
-                        </BButton>
-                    </div>
-                </div>
-            </div>
-        </BTab>
-        <BTab>
-            <template v-slot:title>
-                <FontAwesomeIcon :icon="faUpload" fixed-width />
-                <span>{{ localize("Upload Files to Add to Collection") }}</span>
-            </template>
-            <!-- TODO: This is incomplete; need to return uploadValues to parent -->
-            <DefaultBox
-                v-if="configOptions && extensionsSet"
-                :chunk-upload-size="configOptions.chunkUploadSize"
-                :default-db-key="configOptions.defaultDbKey"
-                :default-extension="defaultExtension"
-                :effective-extensions="props.extensions?.length ? validExtensions : listExtensions"
-                :file-sources-configured="configOptions.fileSourcesConfigured"
-                :ftp-upload-site="ftpUploadSite"
-                :has-callback="false"
-                :history-id="historyId"
-                :list-db-keys="[]"
-                disable-footer
-                emit-uploaded
-                @uploaded="addUploadedFiles"
-                @dismiss="currentTab = Tabs.create">
-                <template v-slot:footer>
-                    <div class="d-flex align-items-center justify-content-between mt-2">
-                        <BAlert v-if="extensions?.length" class="w-100 py-0" variant="secondary" show>
-                            <HelpText
-                                uri="galaxy.collections.collectionBuilder.requiredUploadExtensions"
-                                :text="localize('Required extensions: ')" />
-                            <strong>{{ orList(extensions) }}</strong>
-                        </BAlert>
-                    </div>
-                </template>
-                <template v-slot:emit-btn-txt>
-                    <FontAwesomeIcon :icon="faPlus" fixed-width />
-                    {{ localize("Add Uploaded") }}
-                </template>
-            </DefaultBox>
-        </BTab>
-    </BTabs>
+                    </template>
+                    <template v-slot:emit-btn-txt>
+                        <FontAwesomeIcon :icon="faPlus" fixed-width />
+                        {{ localize("Add Uploaded") }}
+                    </template>
+                </DefaultBox>
+            </BTab>
+        </BTabs>
+    </span>
 </template>
 
 <style lang="scss">
diff --git a/client/src/components/Collections/common/CollectionCreatorFooterButtons.vue b/client/src/components/Collections/common/CollectionCreatorFooterButtons.vue
new file mode 100644
index 00000000000..3137ade35ad
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionCreatorFooterButtons.vue
@@ -0,0 +1,27 @@
+<script setup lang="ts">
+import localize from "@/utils/localization";
+
+interface Props {
+    validInput: boolean;
+    shortWhatIsBeingCreated: string;
+}
+
+defineProps<Props>();
+
+const emit = defineEmits<{
+    (e: "clicked-create"): void;
+    (e: "clicked-cancel"): void;
+}>();
+</script>
+
+<template>
+    <div class="actions vertically-spaced d-flex justify-content-between">
+        <BButton tabindex="-1" @click="emit('clicked-cancel')">
+            {{ localize("Cancel") }}
+        </BButton>
+
+        <BButton class="create-collection" variant="primary" :disabled="!validInput" @click="emit('clicked-create')">
+            {{ localize("Create " + shortWhatIsBeingCreated) }}
+        </BButton>
+    </div>
+</template>
diff --git a/client/src/components/Collections/common/CollectionCreatorHelpHeader.vue b/client/src/components/Collections/common/CollectionCreatorHelpHeader.vue
new file mode 100644
index 00000000000..2564230253d
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionCreatorHelpHeader.vue
@@ -0,0 +1,50 @@
+<script setup lang="ts">
+import { faChevronDown, faChevronUp } from "@fortawesome/free-solid-svg-icons";
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { ref } from "vue";
+
+import localize from "@/utils/localization";
+
+const isExpanded = ref(false);
+
+function clickForHelp() {
+    isExpanded.value = !isExpanded.value;
+    return isExpanded.value;
+}
+</script>
+
+<template>
+    <div class="header flex-row no-flex">
+        <div class="main-help well clear" :class="{ expanded: isExpanded }">
+            <a
+                class="more-help"
+                href="javascript:void(0);"
+                role="button"
+                :title="localize('Expand or Close Help')"
+                @click="clickForHelp">
+                <div v-if="!isExpanded">
+                    <FontAwesomeIcon :icon="faChevronDown" />
+                    <span class="sr-only">{{ localize("Expand Help") }}</span>
+                </div>
+                <div v-else>
+                    <FontAwesomeIcon :icon="faChevronUp" />
+                    <span class="sr-only">{{ localize("Close Help") }}</span>
+                </div>
+            </a>
+
+            <div class="help-content">
+                <!-- each collection that extends this will add their own help content -->
+                <slot></slot>
+
+                <a
+                    class="more-help"
+                    href="javascript:void(0);"
+                    role="button"
+                    :title="localize('Expand or Close Help')"
+                    @click="clickForHelp">
+                    <span class="sr-only">{{ localize("Expand Help") }}</span>
+                </a>
+            </div>
+        </div>
+    </div>
+</template>
diff --git a/client/src/components/Collections/common/CollectionCreatorNoItemsMessage.vue b/client/src/components/Collections/common/CollectionCreatorNoItemsMessage.vue
new file mode 100644
index 00000000000..b525f3a2836
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionCreatorNoItemsMessage.vue
@@ -0,0 +1,18 @@
+<script setup lang="ts">
+import { BAlert, BLink } from "bootstrap-vue";
+
+import localize from "@/utils/localization";
+
+const emit = defineEmits<{
+    (e: "clicked-upload"): void;
+}>();
+</script>
+<template>
+    <BAlert variant="info" show>
+        {{ localize("No items available to create a collection.") }}
+        {{ localize("Exit and change your current history, or") }}
+        <BLink class="text-decoration-none" @click.stop.prevent="emit('clicked-upload')">
+            {{ localize("Upload some datasets.") }}
+        </BLink>
+    </BAlert>
+</template>
diff --git a/client/src/components/Collections/common/CollectionCreatorShowExtensions.vue b/client/src/components/Collections/common/CollectionCreatorShowExtensions.vue
new file mode 100644
index 00000000000..45a99b22eef
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionCreatorShowExtensions.vue
@@ -0,0 +1,25 @@
+<script setup lang="ts">
+import { BAlert } from "bootstrap-vue";
+
+import localize from "@/utils/localization";
+import { orList } from "@/utils/strings";
+
+import HelpText from "@/components/Help/HelpText.vue";
+
+interface Props {
+    extensions?: string[];
+}
+
+defineProps<Props>();
+</script>
+
+<template>
+    <div class="d-flex align-items-center justify-content-between">
+        <BAlert v-if="extensions?.length" class="w-100 py-0" variant="secondary" show>
+            <HelpText
+                uri="galaxy.collections.collectionBuilder.filteredExtensions"
+                :text="localize('Filtered extensions: ')" />
+            <strong>{{ orList(extensions) }}</strong>
+        </BAlert>
+    </div>
+</template>
diff --git a/client/src/components/Collections/common/CollectionCreatorSourceOptions.vue b/client/src/components/Collections/common/CollectionCreatorSourceOptions.vue
new file mode 100644
index 00000000000..c35c4bd7e77
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionCreatorSourceOptions.vue
@@ -0,0 +1,56 @@
+<script setup lang="ts">
+import { BFormCheckbox, BFormGroup } from "bootstrap-vue";
+import { ref, watch } from "vue";
+
+import localize from "@/utils/localization";
+
+import HelpText from "@/components/Help/HelpText.vue";
+
+interface Props {
+    value: boolean;
+    extensionsToggle?: boolean;
+    renderExtensionsToggle?: boolean;
+}
+
+const props = defineProps<Props>();
+
+const localHideSourceItems = ref(props.value);
+
+const emit = defineEmits<{
+    (e: "input", value: boolean): void;
+    (e: "remove-extensions-toggle"): void;
+}>();
+
+// Watch for external updates to value and sync with innerValue
+watch(
+    () => props.value,
+    (newValue) => {
+        localHideSourceItems.value = newValue;
+    }
+);
+
+watch(localHideSourceItems, (newValue) => {
+    emit("input", newValue);
+});
+</script>
+
+<template>
+    <BFormGroup class="inputs-form-group">
+        <BFormCheckbox
+            v-if="renderExtensionsToggle"
+            name="remove-extensions"
+            switch
+            :checked="extensionsToggle"
+            @input="emit('remove-extensions-toggle')">
+            {{ localize("Remove file extensions?") }}
+        </BFormCheckbox>
+
+        <div data-description="hide original elements">
+            <BFormCheckbox v-model="localHideSourceItems" name="hide-originals" switch>
+                <HelpText
+                    uri="galaxy.collections.collectionBuilder.hideOriginalElements"
+                    :text="localize('Hide original elements')" />
+            </BFormCheckbox>
+        </div>
+    </BFormGroup>
+</template>
diff --git a/client/src/components/Collections/common/CollectionNameInput.vue b/client/src/components/Collections/common/CollectionNameInput.vue
new file mode 100644
index 00000000000..7f299899efb
--- /dev/null
+++ b/client/src/components/Collections/common/CollectionNameInput.vue
@@ -0,0 +1,47 @@
+<script setup lang="ts">
+import { BFormGroup, BFormInput } from "bootstrap-vue";
+import { ref, watch } from "vue";
+
+import localize from "@/utils/localization";
+
+interface Props {
+    value: string;
+    shortWhatIsBeingCreated: string;
+}
+
+const props = defineProps<Props>();
+
+const name = ref(props.value);
+
+const emit = defineEmits<{
+    (e: "input", value: string): void;
+}>();
+
+// Watch for external updates to value and sync with innerValue
+watch(
+    () => props.value,
+    (newValue) => {
+        name.value = newValue;
+    }
+);
+
+watch(name, (newValue) => {
+    emit("input", newValue);
+});
+</script>
+
+<template>
+    <BFormGroup
+        class="flex-gapx-1 d-flex align-items-center w-50 inputs-form-group"
+        :label="localize('Name:')"
+        label-for="collection-name">
+        <BFormInput
+            id="collection-name"
+            v-model="name"
+            class="collection-name"
+            :placeholder="localize('Enter a name for your new ' + shortWhatIsBeingCreated)"
+            size="sm"
+            required
+            :state="!name ? false : null" />
+    </BFormGroup>
+</template>
diff --git a/client/src/components/DatasetInformation/DatasetError.vue b/client/src/components/DatasetInformation/DatasetError.vue
index cbe9f3e4018..22a807219ae 100644
--- a/client/src/components/DatasetInformation/DatasetError.vue
+++ b/client/src/components/DatasetInformation/DatasetError.vue
@@ -9,6 +9,7 @@ import { computed, onMounted, ref } from "vue";
 import { GalaxyApi, type HDADetailed } from "@/api";
 import { fetchDatasetDetails } from "@/api/datasets";
 import { type JobDetails, type JobInputSummary } from "@/api/jobs";
+import { useConfig } from "@/composables/config";
 import { useMarkdown } from "@/composables/markdown";
 import { useUserStore } from "@/stores/userStore";
 import localize from "@/utils/localization";
@@ -30,6 +31,7 @@ const userStore = useUserStore();
 const { currentUser } = storeToRefs(userStore);
 
 const { renderMarkdown } = useMarkdown({ openLinksInNewPage: true });
+const { config, isConfigLoaded } = useConfig();
 
 const message = ref("");
 const jobLoading = ref(true);
@@ -47,6 +49,8 @@ const showForm = computed(() => {
     return noResult || hasError;
 });
 
+const showWizard = computed(() => isConfigLoaded && config.value?.llm_api_configured);
+
 async function getDatasetDetails() {
     datasetLoading.value = true;
     try {
@@ -154,21 +158,22 @@ onMounted(async () => {
                 <b id="dataset-error-tool-id" class="text-break">{{ jobDetails.tool_id }}</b
                 >.
             </p>
-
-            <h4 class="mb-3 h-md">Possible Causes</h4>
-            <p>
-                <span>
-                    We can use AI to analyze the issue and suggest possible fixes. Please note that the diagnosis may
-                    not always be accurate.
-                </span>
-            </p>
-            <BCard class="mb-2">
-                <GalaxyWizard
-                    view="error"
-                    :query="jobDetails.tool_stderr"
-                    context="tool_error"
-                    :job-id="jobDetails.id" />
-            </BCard>
+            <template v-if="showWizard">
+                <h4 class="mb-3 h-md">Possible Causes</h4>
+                <p>
+                    <span>
+                        We can use AI to analyze the issue and suggest possible fixes. Please note that the diagnosis
+                        may not always be accurate.
+                    </span>
+                </p>
+                <BCard class="mb-2">
+                    <GalaxyWizard
+                        view="error"
+                        :query="jobDetails.tool_stderr"
+                        context="tool_error"
+                        :job-id="jobDetails.id" />
+                </BCard>
+            </template>
 
             <DatasetErrorDetails
                 :tool-stderr="jobDetails.tool_stderr"
diff --git a/client/src/components/JobInformation/JobInformation.test.js b/client/src/components/JobInformation/JobInformation.test.js
index 8cc65b9499c..1092c0e422a 100644
--- a/client/src/components/JobInformation/JobInformation.test.js
+++ b/client/src/components/JobInformation/JobInformation.test.js
@@ -69,8 +69,8 @@ describe("JobInformation/JobInformation.vue", () => {
         // table should exist
         expect(jobInfoTable).toBeTruthy();
         const rows = jobInfoTable.findAll("tr");
-        // should contain 9 rows
-        expect(rows.length).toBe(9);
+        // should contain 10 rows
+        expect(rows.length).toBe(10);
     });
 
     it("stdout and stderr should be rendered", async () => {
@@ -98,5 +98,6 @@ describe("JobInformation/JobInformation.vue", () => {
             { id: "encoded-copied-from-job-id", backend_key: "copied_from_job_id" },
         ];
         verifyValues(rendered_entries, jobInfoTable, jobResponse);
+        expect(wrapper.find('td[data-description="galaxy-job-state"]').exists()).toBe(true);
     });
 });
diff --git a/client/src/components/JobInformation/JobInformation.vue b/client/src/components/JobInformation/JobInformation.vue
index 22871692e6f..8e63e8dea2e 100644
--- a/client/src/components/JobInformation/JobInformation.vue
+++ b/client/src/components/JobInformation/JobInformation.vue
@@ -39,11 +39,15 @@ const stderr_position = computed(() => stderr_text.value.length);
 const runTime = computed(() => getJobDuration(job.value));
 
 function jobStateIsTerminal(jobState) {
-    return jobState && !NON_TERMINAL_STATES.includes(job.value.state);
+    return jobState && !NON_TERMINAL_STATES.includes(jobState);
+}
+
+function jobStateIsRunning(jobState) {
+    return jobState == "running";
 }
 
 const jobIsTerminal = computed(() => jobStateIsTerminal(job?.value?.state));
-
+const jobIsRunning = computed(() => jobStateIsRunning(job?.value?.state));
 const routeToInvocation = computed(() => `/workflows/invocations/${invocationId.value}`);
 
 const metadataDetail = ref({
@@ -127,6 +131,7 @@ watch(
     <div>
         <JobDetailsProvider auto-refresh :job-id="props.job_id" @update:result="updateJob" />
         <JobConsoleOutputProvider
+            v-if="jobIsRunning"
             auto-refresh
             :job-id="props.job_id"
             :stdout_position="stdout_position"
diff --git a/client/src/components/JobInformation/testData/jobInformationResponse.json b/client/src/components/JobInformation/testData/jobInformationResponse.json
index a53d9efa910..4a74f832272 100644
--- a/client/src/components/JobInformation/testData/jobInformationResponse.json
+++ b/client/src/components/JobInformation/testData/jobInformationResponse.json
@@ -7,5 +7,6 @@
     "command_line": "commandline",
     "job_messages": ["test-msg1", "test-msg2", "test-msg3", "test-msg4"],
     "id": "test_id",
-    "copied_from_job_id": "test_copied_from_job_id"
+    "copied_from_job_id": "test_copied_from_job_id",
+    "state": "running"
 }
diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 14bc863f19c..462220c0ddd 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -1102,8 +1102,9 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
 
         self._process_celery_config()
 
-        # load in the chat_prompts if openai is enabled
-        self._load_chat_prompts()
+        # load in the chat_prompts if openai api key is configured
+        if self.openai_api_key:
+            self._load_chat_prompts()
 
         self.pretty_datetime_format = expand_pretty_datetime_format(self.pretty_datetime_format)
         try:
@@ -1266,21 +1267,20 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
             self.file_source_temp_dir = os.path.abspath(self.file_source_temp_dir)
 
     def _load_chat_prompts(self):
-        if self.openai_api_key:
-            current_dir = os.path.dirname(os.path.abspath(__file__))
-            chat_prompts_path = os.path.join(current_dir, "chat_prompts.json")
+        current_dir = os.path.dirname(os.path.abspath(__file__))
+        chat_prompts_path = os.path.join(current_dir, "chat_prompts.json")
 
-            if os.path.exists(chat_prompts_path):
-                try:
-                    with open(chat_prompts_path, encoding="utf-8") as file:
-                        data = json.load(file)
-                        self.chat_prompts = data.get("prompts", {})
-                except json.JSONDecodeError as e:
-                    log.error(f"JSON decoding error in chat prompts file: {e}")
-                except Exception as e:
-                    log.error(f"An error occurred while reading chat prompts file: {e}")
-            else:
-                log.warning(f"Chat prompts file not found at {chat_prompts_path}")
+        if os.path.exists(chat_prompts_path):
+            try:
+                with open(chat_prompts_path, encoding="utf-8") as file:
+                    data = json.load(file)
+                    self.chat_prompts = data.get("prompts", {})
+            except json.JSONDecodeError as e:
+                log.error(f"JSON decoding error in chat prompts file: {e}")
+            except Exception as e:
+                log.error(f"An error occurred while reading chat prompts file: {e}")
+        else:
+            log.warning(f"Chat prompts file not found at {chat_prompts_path}")
 
     def _process_celery_config(self):
         if self.celery_conf and self.celery_conf.get("result_backend") is None:
diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index b51d3768f21..a1f47b3147e 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -849,7 +849,11 @@ class Data(metaclass=DataMeta):
         job, converted_datasets, *_ = converter.execute(
             trans, incoming=params, set_output_hid=visible, history=history, flush_job=False
         )
+        # We should only have a single converted output, but let's be defensive here
+        n_converted_datasets = len(converted_datasets)
         for converted_dataset in converted_datasets.values():
+            if converted_dataset.extension == "auto" and n_converted_datasets == 1:
+                converted_dataset.extension = target_type
             original_dataset.attach_implicitly_converted_dataset(trans.sa_session, converted_dataset, target_type)
         trans.app.job_manager.enqueue(job, tool=converter)
         if len(params) > 0:
diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py
index d0ccfa8d53c..f30118d2fbf 100644
--- a/lib/galaxy/managers/configuration.py
+++ b/lib/galaxy/managers/configuration.py
@@ -229,6 +229,7 @@ class ConfigSerializer(base.ModelSerializer):
             "fixed_delegated_auth": _defaults_to(False),
             "help_forum_api_url": _use_config,
             "enable_help_forum_tool_panel_integration": _use_config,
+            "llm_api_configured": lambda item, key, **context: bool(item.openai_api_key),
         }
 
 
diff --git a/lib/galaxy/tool_util/linters/output.py b/lib/galaxy/tool_util/linters/output.py
index e9ab7c4aaf4..b1d48fd2a60 100644
--- a/lib/galaxy/tool_util/linters/output.py
+++ b/lib/galaxy/tool_util/linters/output.py
@@ -83,9 +83,9 @@ class OutputsFilterExpression(Linter):
         tool_xml = getattr(tool_source, "xml_tree", None)
         if not tool_xml:
             return
-        for filter in tool_xml.findall("./outputs//filter"):
+        for filter in tool_xml.findall("./outputs/*/filter"):
             try:
-                ast.parse(filter.text, mode="eval")
+                ast.parse(filter.text.strip(), mode="eval")
             except Exception as e:
                 lint_ctx.warn(
                     f"Filter '{filter.text}' is no valid expression: {str(e)}",
diff --git a/lib/galaxy/tool_util/parser/parameter_validators.py b/lib/galaxy/tool_util/parser/parameter_validators.py
index 29af9494b0b..f850e0acce8 100644
--- a/lib/galaxy/tool_util/parser/parameter_validators.py
+++ b/lib/galaxy/tool_util/parser/parameter_validators.py
@@ -668,9 +668,9 @@ def raise_error_if_valiation_fails(
         raise AssertionError("Validator logic problem - computed validation value must be boolean")
     if message is None:
         message = validator.message
-    if message is None:
+    if not message:
         message = DEFAULT_VALIDATOR_MESSAGE
-    assert message
+    assert message is not None
     if value_to_show and "%s" in message:
         message = message % value_to_show
     negate = validator.negate
diff --git a/lib/galaxy/tool_util/verify/interactor.py b/lib/galaxy/tool_util/verify/interactor.py
index 7e715538262..7d66d3a49a6 100644
--- a/lib/galaxy/tool_util/verify/interactor.py
+++ b/lib/galaxy/tool_util/verify/interactor.py
@@ -1688,7 +1688,7 @@ def adapt_tool_source_dict(processed_dict: ToolTestDict) -> ToolTestDescriptionD
 
     if not error_in_test_definition:
         processed_test_dict = cast(ValidToolTestDict, processed_dict)
-        maxseconds = _get_maxseconds(processed_test_dict)
+        maxseconds = processed_test_dict.get("maxseconds")
         output_collections = processed_test_dict.get("output_collections", [])
         if "num_outputs" in processed_test_dict and processed_test_dict["num_outputs"]:
             num_outputs = int(processed_test_dict["num_outputs"])
@@ -1750,10 +1750,6 @@ def _get_test_name(test_dict: Union[ToolTestDict, ToolTestDescriptionDict], test
     return name
 
 
-def _get_maxseconds(test_dict: Union[ToolTestDict, ToolTestDescriptionDict]) -> int:
-    return int(cast(Union[str, int], test_dict.get("maxseconds") or DEFAULT_TOOL_TEST_WAIT or 86400))
-
-
 def expanded_inputs_from_json(expanded_inputs_json: ExpandedToolInputsJsonified) -> ExpandedToolInputs:
     loaded_inputs: ExpandedToolInputs = {}
     for key, value in expanded_inputs_json.items():
@@ -1829,7 +1825,7 @@ class ToolTestDescription:
         self.inputs = expanded_inputs_from_json(json_dict.get("inputs", {}))
         self.tool_id = json_dict["tool_id"]
         self.tool_version = json_dict.get("tool_version")
-        self.maxseconds = _get_maxseconds(json_dict)
+        self.maxseconds = json_dict.get("maxseconds")
 
     def test_data(self):
         """
@@ -1839,31 +1835,31 @@ class ToolTestDescription:
 
     def to_dict(self) -> ToolTestDescriptionDict:
         inputs = expanded_inputs_to_json(self.inputs)
-        return ToolTestDescriptionDict(
-            {
-                "inputs": inputs,
-                "outputs": self.outputs,
-                "output_collections": [_.to_dict() for _ in self.output_collections],
-                "num_outputs": self.num_outputs,
-                "command_line": self.command_line,
-                "command_version": self.command_version,
-                "stdout": self.stdout,
-                "stderr": self.stderr,
-                "expect_exit_code": self.expect_exit_code,
-                "expect_failure": self.expect_failure,
-                "expect_test_failure": self.expect_test_failure,
-                "name": self.name,
-                "test_index": self.test_index,
-                "tool_id": self.tool_id,
-                "tool_version": self.tool_version,
-                "required_files": self.required_files,
-                "required_data_tables": self.required_data_tables,
-                "required_loc_files": self.required_loc_files,
-                "error": self.error,
-                "exception": self.exception,
-                "maxseconds": self.maxseconds,
-            }
-        )
+        test_description_def: ToolTestDescriptionDict = {
+            "inputs": inputs,
+            "outputs": self.outputs,
+            "output_collections": [_.to_dict() for _ in self.output_collections],
+            "num_outputs": self.num_outputs,
+            "command_line": self.command_line,
+            "command_version": self.command_version,
+            "stdout": self.stdout,
+            "stderr": self.stderr,
+            "expect_exit_code": self.expect_exit_code,
+            "expect_failure": self.expect_failure,
+            "expect_test_failure": self.expect_test_failure,
+            "name": self.name,
+            "test_index": self.test_index,
+            "tool_id": self.tool_id,
+            "tool_version": self.tool_version,
+            "required_files": self.required_files,
+            "required_data_tables": self.required_data_tables,
+            "required_loc_files": self.required_loc_files,
+            "error": self.error,
+            "exception": self.exception,
+        }
+        if self.maxseconds is not None:
+            test_description_def["maxseconds"] = self.maxseconds
+        return ToolTestDescriptionDict(**test_description_def)
 
 
 def test_data_iter(required_files):
diff --git a/lib/galaxy_test/api/test_tools.py b/lib/galaxy_test/api/test_tools.py
index 41d982d246c..130b9c9c91a 100644
--- a/lib/galaxy_test/api/test_tools.py
+++ b/lib/galaxy_test/api/test_tools.py
@@ -2205,6 +2205,24 @@ class TestToolsApi(ApiTestCase, TestsTools):
                 exception_raised = e
             assert exception_raised, "Expected invalid column selection to fail job"
 
+    @skip_without_tool("implicit_conversion_format_input")
+    def test_implicit_conversion_input_dataset_tracking(self):
+        with self.dataset_populator.test_history() as history_id:
+            compressed_path = self.test_data_resolver.get_filename("1.fastqsanger.gz")
+            with open(compressed_path, "rb") as fh:
+                dataset = self.dataset_populator.new_dataset(
+                    history_id, content=fh, file_type="fastqsanger.gz", wait=True
+                )
+            outputs = self._run(
+                "Grep1", history_id=history_id, inputs={"data": {"src": "hda", "id": dataset["id"]}}, assert_ok=True
+            )
+            job_details = self.dataset_populator.get_job_details(outputs["jobs"][0]["id"], full=True).json()
+            assert job_details["inputs"]["input"]["id"] != dataset["id"]
+            converted_input = self.dataset_populator.get_history_dataset_details(
+                history_id=history_id, content_id=job_details["inputs"]["input"]["id"]
+            )
+            assert converted_input["extension"] == "fastqsanger"
+
     @skip_without_tool("column_multi_param")
     def test_implicit_conversion_and_reduce(self):
         with self.dataset_populator.test_history() as history_id:
diff --git a/test/unit/tool_util/test_test_definition_parsing.py b/test/unit/tool_util/test_test_definition_parsing.py
index 6576660c3b0..ed5fbdaaee9 100644
--- a/test/unit/tool_util/test_test_definition_parsing.py
+++ b/test/unit/tool_util/test_test_definition_parsing.py
@@ -68,6 +68,21 @@ class TestTestParsing(TestCase):
         tool_source = get_tool_source(path)
         self.tool_source = tool_source
 
+    def test_maxseconds_not_filled_with_default(self):
+        self._init_tool_for_path(functional_test_tool_path("simple_constructs.xml"))
+        test_dicts = list(self._parse_tests())
+        assert test_dicts[0].maxseconds is None
+        assert "maxseconds" not in test_dicts[0].to_dict()
+
+    def test_maxseconds_parsed(self):
+        self._init_tool_for_path(functional_test_tool_path("maxseconds.xml"))
+        test_def = next(iter(self._parse_tests()))
+        assert test_def.maxseconds == 5
+        test_dict = test_def.to_dict()
+        print(test_dict)
+        assert "maxseconds" in test_dict
+        assert test_dict["maxseconds"] == 5
+
     def test_simple_state_parsing(self):
         self._init_tool_for_path(functional_test_tool_path("simple_constructs.xml"))
         test_dicts = self._parse_tests()
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index c8dbcda5d4a..241b81e1864 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -700,7 +700,7 @@ OUTPUTS_FILTER_EXPRESSION = """
     <outputs>
         <data name="another_valid_name" format="fasta" label="a label">
             <filter>an invalid condition</filter>
-            <filter>an and condition</filter>
+            <filter> an and condition </filter>
         </data>
         <collection name="yet_another_valid_name" type="list" format="fasta" label="another label">
             <filter>another invalid condition</filter>