diff --git a/client/src/components/Form/Elements/FormData/FormData.vue b/client/src/components/Form/Elements/FormData/FormData.vue
index f6054f28cd00..64b5d62dec2b 100644
--- a/client/src/components/Form/Elements/FormData/FormData.vue
+++ b/client/src/components/Form/Elements/FormData/FormData.vue
@@ -5,6 +5,7 @@ import { faCaretDown, faCaretUp, faExclamation, faLink, faUnlink } from "@fortaw
 import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
 import { BAlert, BButton, BButtonGroup, BCollapse, BFormCheckbox, BTooltip } from "bootstrap-vue";
 import { computed, onMounted, type Ref, ref, watch } from "vue";
+import HelpText from "@/components/Help/HelpText.vue";
 
 import { getGalaxyInstance } from "@/app";
 import { useDatatypesMapper } from "@/composables/datatypesMapper";
@@ -650,7 +651,10 @@ const noOptionsWarningMessage = computed(() => {
             </BFormCheckbox>
             <div class="info text-info">
                 <FontAwesomeIcon icon="fa-exclamation" />
-                <span v-localize class="ml-1">
+                <span class="ml-1" v-if="props.type == 'data' && currentVariant.src == SOURCE.COLLECTION">
+                    The supplied input will be <HelpText text="mapped over" uri="galaxy.collections.mapOver" /> this tool.
+                </span>
+                <span v-localize class="ml-1" v-else>
                     This is a batch mode input field. Individual jobs will be triggered for each dataset.
                 </span>
             </div>
diff --git a/client/src/components/Help/HelpPopover.vue b/client/src/components/Help/HelpPopover.vue
new file mode 100644
index 000000000000..637dea8ebe95
--- /dev/null
+++ b/client/src/components/Help/HelpPopover.vue
@@ -0,0 +1,20 @@
+<script setup lang="ts">
+import ConfigurationMarkdown from "@/components/ObjectStore/ConfigurationMarkdown.vue";
+
+interface Props {
+    target: any;
+    help: string;
+}
+
+defineProps<Props>();
+</script>
+
+
+<template>
+    <b-popover
+        :target="target"
+        triggers="hover"
+        placement="bottom">
+        <ConfigurationMarkdown :markdown="help" :admin="true" />
+    </b-popover>
+</template>
diff --git a/client/src/components/Help/HelpText.vue b/client/src/components/Help/HelpText.vue
index f3f1b4740af1..24e166f97c78 100644
--- a/client/src/components/Help/HelpText.vue
+++ b/client/src/components/Help/HelpText.vue
@@ -1,9 +1,9 @@
 <script setup lang="ts">
-import { computed } from "vue";
+import { toRef } from "vue";
 
-import { hasHelp as hasHelpText, help as helpText } from "./terms";
+import { useHelp } from "./useHelp";
 
-import ConfigurationMarkdown from "@/components/ObjectStore/ConfigurationMarkdown.vue";
+import HelpPopover from "./HelpPopover.vue";
 
 interface Props {
     uri: string;
@@ -12,28 +12,19 @@ interface Props {
 
 const props = defineProps<Props>();
 
-const hasHelp = computed<boolean>(() => {
-    return hasHelpText(props.uri);
-});
-
-const help = computed<string>(() => {
-    return helpText(props.uri) as string;
-});
+const { hasHelp, help } = useHelp(toRef(props, "uri"));
 </script>
 
 <template>
     <span>
-        <b-popover
+        <HelpPopover
             v-if="hasHelp"
             :target="
                 () => {
                     return $refs.helpTarget;
                 }
             "
-            triggers="hover"
-            placement="bottom">
-            <ConfigurationMarkdown :markdown="help" :admin="true" />
-        </b-popover>
+            :help="help" />
         <span v-if="hasHelp" ref="helpTarget" class="help-text">{{ text }}</span>
         <span v-else>{{ text }}</span>
     </span>
diff --git a/client/src/components/Help/terms.yml b/client/src/components/Help/terms.yml
index a6df4b852a63..6391c7979e18 100644
--- a/client/src/components/Help/terms.yml
+++ b/client/src/components/Help/terms.yml
@@ -29,6 +29,31 @@ unix:
     More information on stack traces can be found on [Wikipedia](https://en.wikipedia.org/wiki/Stack_trace).
 
 galaxy:
+  collections:
+    flatList: |
+      A flat list is just a simple dataset collection of type ``list`` that contains only datasets and not
+      other collections.
+    mapOver: |
+      When a tool consumes a dataset but is run with a collection, the collection *maps over* the collection.
+      This means instead of just running the tool once - the tool will be run once for each element of the
+      provided collection. Additionally, the outputs of the tool will be collected into a collection that
+      matches the structure of the provided collection. This matching structure means the output collections
+      will have the same element identifiers as the provided collection and they will appear in the same order.
+
+      It is easiest to visualize "mapping over" a collection is in the context of a tool that consumes a dataset
+      and produces a dataset, but the semantics apply rather naturally to tools that consume collections or
+      produce collections as well.
+      
+      For instance, consider a tool that consumes a ``paired`` collection and produces an output dataset.
+      If a list of paired collections (collection type ``list:paired``) is passed to the tool - it will
+      will produce a flat list (collection type ``list``) of output datasets with the same number of elements
+      in the same order as the provided list of ``paired`` collections.
+
+      In the case of outputs, consider a tool that takes in a dataset and produces a flat list. If this tool
+      is run over a flat list of datasets - that list will be "mapped over" and each element will produce a list.
+      These lists will be gathered together in a nested list structured (collection type ``list:list``) where
+      the outer element count and structure matches that of the input and the inner list for each of those
+      is just the outputs of the tool for the corresponding element of the input.
   jobs:
     states:
       # upload, waiting, failed, paused, deleting, deleted, stop, stopped, skipped.
diff --git a/client/src/components/Help/useHelp.ts b/client/src/components/Help/useHelp.ts
new file mode 100644
index 000000000000..d9fbd92f383e
--- /dev/null
+++ b/client/src/components/Help/useHelp.ts
@@ -0,0 +1,17 @@
+import { computed,type Ref } from "vue";
+
+import { hasHelp as hasHelpText, help as helpText } from "./terms";
+
+export function useHelp(
+    uri: Ref<string>,
+) {
+    const hasHelp = computed<boolean>(() => {
+        return hasHelpText(uri.value);
+    });
+    
+    const help = computed<string>(() => {
+        return helpText(uri.value) as string;
+    });
+
+    return { hasHelp, help };
+}
diff --git a/client/src/components/Tool/ToolCard.vue b/client/src/components/Tool/ToolCard.vue
index d28e4d46ad96..6c0876d3ac8c 100644
--- a/client/src/components/Tool/ToolCard.vue
+++ b/client/src/components/Tool/ToolCard.vue
@@ -186,7 +186,7 @@ const showHelpForum = computed(() => isConfigLoaded.value && config.value.enable
         <div>
             <div v-if="props.options.help" class="mt-2 mb-4">
                 <Heading h2 separator bold size="sm"> Help </Heading>
-                <ToolHelp :content="props.options.help" />
+                <ToolHelp :content="props.options.help" :type="props.options.help_type" />
             </div>
 
             <ToolTutorialRecommendations
diff --git a/client/src/components/Tool/ToolHelp.vue b/client/src/components/Tool/ToolHelp.vue
index 88420b8b2ee6..eb95dd730460 100644
--- a/client/src/components/Tool/ToolHelp.vue
+++ b/client/src/components/Tool/ToolHelp.vue
@@ -1,42 +1,19 @@
-<script setup>
-import { useFormattedToolHelp } from "composables/formattedToolHelp";
+<script setup lang="ts">
+import ToolHelpMarkdown from "./ToolHelpMarkdown.vue";
+import ToolHelpRst from "./ToolHelpRst.vue";
 
-const props = defineProps({
-    content: {
-        type: String,
-        required: true,
-    },
-});
+defineProps<{
+    type: string;
+    content: string;
+}>();
 
-const { formattedContent } = useFormattedToolHelp(props.content);
 </script>
-
 <template>
-    <div class="form-help form-text" v-html="formattedContent" />
+    <span>
+        <ToolHelpMarkdown v-if="type=='markdown'" :content="content" />
+        <ToolHelpRst v-else-if="type=='restructuredtext'" :content="content" />
+        <div v-else class="form-help form-text">
+            {{ content }}
+        </div>
+    </span>
 </template>
-
-<style lang="scss" scoped>
-@import "scss/theme/blue.scss";
-
-.form-help {
-    &:deep(h3) {
-        font-size: $h4-font-size;
-        font-weight: bold;
-    }
-
-    &:deep(h4) {
-        font-size: $h5-font-size;
-        font-weight: bold;
-    }
-
-    &:deep(h5) {
-        font-size: $h6-font-size;
-        font-weight: bold;
-    }
-
-    &:deep(h6) {
-        font-size: $h6-font-size;
-        text-decoration: underline;
-    }
-}
-</style>
diff --git a/client/src/components/Tool/ToolHelpMarkdown.vue b/client/src/components/Tool/ToolHelpMarkdown.vue
new file mode 100644
index 000000000000..15cee791dfb0
--- /dev/null
+++ b/client/src/components/Tool/ToolHelpMarkdown.vue
@@ -0,0 +1,64 @@
+<script setup lang="ts">
+import { computed, onMounted, ref } from "vue";
+
+import { hasHelp, help } from "@/components/Help/terms";
+import { markup } from "@/components/ObjectStore/configurationMarkdown";
+import { useFormattedToolHelp } from "@/composables/formattedToolHelp";
+
+import HelpPopover from "@/components/Help/HelpPopover.vue";
+
+const props = defineProps<{
+    content: string;
+}>();
+
+const markdownHtml = computed(() => markup(props.content ?? "", false));
+// correct links and header information... this should work the same between rst and
+// markdown entirely I think.
+const { formattedContent } = useFormattedToolHelp(markdownHtml);
+
+const helpHtml = ref<HTMLDivElement>();
+
+interface InternalTypeReference {
+    element: HTMLElement;
+    markdown: string;
+}
+
+const internalHelpReferences = ref<InternalTypeReference[]>([]);
+
+function setupPopovers() {
+    internalHelpReferences.value.length = 0;
+    if (helpHtml.value) {
+        const links = helpHtml.value.getElementsByTagName("a");
+        Array.from(links).forEach((link) => {
+            if (link.href.startsWith("help://")) {
+                const uri = link.href.substr("help://".length);
+                if( hasHelp(uri)) {
+                    const helpMarkdown = help(uri);
+                    internalHelpReferences.value.push({element: link, markdown: helpMarkdown});
+                }
+                link.href = "#";
+                link.style.color = "inherit";
+                link.style.textDecorationLine = "underline";
+                link.style.textDecorationStyle = "dashed";
+            }
+        });
+    }
+}
+
+onMounted(setupPopovers);
+</script>
+
+
+<template>
+    <span>
+        <!-- Disable v-html warning because we allow markdown generated HTML
+            in various places in the Galaxy interface. Raw HTML is not allowed
+            here because admin = false in the call to markup.
+        -->
+        <!-- eslint-disable-next-line vue/no-v-html -->
+        <div ref="helpHtml" v-html="formattedContent" />
+        <span v-for="(value, i) in internalHelpReferences" v:key="i">
+            <HelpPopover :target="value.element" :help="value.markdown" />
+        </span>
+    </span>
+</template>
diff --git a/client/src/components/Tool/ToolHelp.test.js b/client/src/components/Tool/ToolHelpRst.test.js
similarity index 87%
rename from client/src/components/Tool/ToolHelp.test.js
rename to client/src/components/Tool/ToolHelpRst.test.js
index afbd19d4ba92..40f8e95f2d1e 100644
--- a/client/src/components/Tool/ToolHelp.test.js
+++ b/client/src/components/Tool/ToolHelpRst.test.js
@@ -1,7 +1,7 @@
 import { mount } from "@vue/test-utils";
 import { getLocalVue } from "tests/jest/helpers";
 
-import ToolHelp from "./ToolHelp";
+import ToolHelpRst from "./ToolHelpRst";
 
 const localVue = getLocalVue();
 
@@ -25,9 +25,9 @@ const expectedHelpText = `
 <h6>h4 Heading</h6>
 <a target="_blank">empty link</a>`;
 
-describe("ToolHelp", () => {
+describe("ToolHelp RST", () => {
     it("modifies help text", () => {
-        const wrapper = mount(ToolHelp, {
+        const wrapper = mount(ToolHelpRst, {
             propsData: {
                 content: inputHelpText,
             },
diff --git a/client/src/components/Tool/ToolHelpRst.vue b/client/src/components/Tool/ToolHelpRst.vue
new file mode 100644
index 000000000000..88420b8b2ee6
--- /dev/null
+++ b/client/src/components/Tool/ToolHelpRst.vue
@@ -0,0 +1,42 @@
+<script setup>
+import { useFormattedToolHelp } from "composables/formattedToolHelp";
+
+const props = defineProps({
+    content: {
+        type: String,
+        required: true,
+    },
+});
+
+const { formattedContent } = useFormattedToolHelp(props.content);
+</script>
+
+<template>
+    <div class="form-help form-text" v-html="formattedContent" />
+</template>
+
+<style lang="scss" scoped>
+@import "scss/theme/blue.scss";
+
+.form-help {
+    &:deep(h3) {
+        font-size: $h4-font-size;
+        font-weight: bold;
+    }
+
+    &:deep(h4) {
+        font-size: $h5-font-size;
+        font-weight: bold;
+    }
+
+    &:deep(h5) {
+        font-size: $h6-font-size;
+        font-weight: bold;
+    }
+
+    &:deep(h6) {
+        font-size: $h6-font-size;
+        text-decoration: underline;
+    }
+}
+</style>
diff --git a/lib/galaxy/tool_util/parser/cwl.py b/lib/galaxy/tool_util/parser/cwl.py
index 571a7faa4172..6891dd9590c6 100644
--- a/lib/galaxy/tool_util/parser/cwl.py
+++ b/lib/galaxy/tool_util/parser/cwl.py
@@ -11,6 +11,7 @@
 )
 from galaxy.tool_util.deps import requirements
 from .interface import (
+    HelpContent,
     PageSource,
     PagesSource,
     ToolSource,
@@ -80,7 +81,11 @@ def parse_edam_topics(self):
         return []
 
     def parse_help(self):
-        return self.tool_proxy.doc()
+        doc = self.tool_proxy.doc()
+        if doc:
+            return HelpContent(type="plain_text", content=doc)
+        else:
+            return None
 
     def parse_sanitize(self):
         return False
diff --git a/lib/galaxy/tool_util/parser/interface.py b/lib/galaxy/tool_util/parser/interface.py
index a7b3896c289f..f0f06103e80d 100644
--- a/lib/galaxy/tool_util/parser/interface.py
+++ b/lib/galaxy/tool_util/parser/interface.py
@@ -121,6 +121,11 @@ class Citation(BaseModel):
     content: str
 
 
+class HelpContent(BaseModel):
+    type: Literal["restructuredtext", "plain_text", "markdown"]
+    content: str
+
+
 class ToolSource(metaclass=ABCMeta):
     """This interface represents an abstract source to parse tool
     information from.
@@ -333,9 +338,11 @@ def parse_stdio(self):
         return [], []
 
     @abstractmethod
-    def parse_help(self) -> Optional[str]:
-        """Return RST definition of help text for tool or None if the tool
-        doesn't define help text.
+    def parse_help(self) -> Optional[HelpContent]:
+        """Return help text for tool or None if the tool doesn't define help text.
+
+        The returned object contains the help text and an indication if it ``rst``
+        or ``markdown``.
         """
 
     @abstractmethod
diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index 9ab4a30f65b6..a84ece1156c0 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -41,6 +41,7 @@
     DrillDownDynamicOptions,
     DrillDownOptionsDict,
     DynamicOptions,
+    HelpContent,
     InputSource,
     PageSource,
     PagesSource,
@@ -649,9 +650,14 @@ def parse_strict_shell(self):
         else:
             return string_as_bool(default)
 
-    def parse_help(self):
+    def parse_help(self) -> Optional[HelpContent]:
         help_elem = self.root.find("help")
-        return help_elem.text if help_elem is not None else None
+        if help_elem is None:
+            return None
+
+        help_type = help_elem.get("type", "restructuredtext")
+        content = help_elem.text
+        return HelpContent(type=help_type, content=content)
 
     @property
     def macro_paths(self):
diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py
index 6813db0f5211..1f3f7976e724 100644
--- a/lib/galaxy/tool_util/parser/yaml.py
+++ b/lib/galaxy/tool_util/parser/yaml.py
@@ -125,7 +125,11 @@ def parse_stdio(self):
         return error_on_exit_code()
 
     def parse_help(self):
-        return self.root_dict.get("help", None)
+        content = self.root_dict.get("help", None)
+        if content:
+            return HelpContent(type="markdown", content=content)
+        else:
+            return None
 
     def parse_outputs(self, tool):
         outputs = self.root_dict.get("outputs", {})
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 7193fd6ea618..81d6940db560 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -78,6 +78,7 @@
     ToolOutputCollectionPart,
 )
 from galaxy.tool_util.parser.interface import (
+    HelpContent,
     InputSource,
     PageSource,
     ToolSource,
@@ -1678,9 +1679,10 @@ def populate_tool_shed_info(self, tool_shed_repository):
 
     @property
     def help(self) -> Template:
+        assert self.raw_help.type == "restructuredtext"
         try:
             return Template(
-                rst_to_html(self.raw_help),
+                rst_to_html(self.raw_help.content),
                 input_encoding="utf-8",
                 default_filters=["decode.utf8"],
                 encoding_errors="replace",
@@ -1697,23 +1699,25 @@ def biotools_reference(self) -> Optional[str]:
         """
         return biotools_reference(self.xrefs)
 
-    def __get_help_with_images(self, raw_help: Optional[str]):
-        help_text = raw_help or ""
-        try:
-            if help_text.find(".. image:: ") >= 0 and (self.tool_shed_repository or self.repository_id):
-                return set_image_paths(
-                    self.app,
-                    help_text,
-                    encoded_repository_id=self.repository_id,
-                    tool_shed_repository=self.tool_shed_repository,
-                    tool_id=self.old_id,
-                    tool_version=self.version,
+    def __get_help_with_images(self, help_content: Optional[HelpContent]) -> Optional[HelpContent]:
+        if help_content and help_content.type == "restructuredtext":
+            help_text = help_content.content or ""
+            try:
+                if help_text.find(".. image:: ") >= 0 and (self.tool_shed_repository or self.repository_id):
+                    help_text = set_image_paths(
+                        self.app,
+                        help_text,
+                        encoded_repository_id=self.repository_id,
+                        tool_shed_repository=self.tool_shed_repository,
+                        tool_id=self.old_id,
+                        tool_version=self.version,
+                    )
+            except Exception:
+                log.exception(
+                    "Exception in parse_help, so images may not be properly displayed for tool with id '%s'", self.id
                 )
-        except Exception:
-            log.exception(
-                "Exception in parse_help, so images may not be properly displayed for tool with id '%s'", self.id
-            )
-        return help_text
+            help_content = HelpContent(type="restructuredtext", content=help_text)
+        return help_content
 
     def find_output_def(self, name):
         # name is JobToOutputDatasetAssociation name.
@@ -2505,12 +2509,17 @@ def to_dict(self, trans, link_details=False, io_details=False, tool_help=False):
         if tool_help:
             # create tool help
             help_txt = ""
-            if self.help:
-                help_txt = self.help.render(
-                    static_path=self.app.url_for("/static"), host_url=self.app.url_for("/", qualified=True)
-                )
-                help_txt = unicodify(help_txt)
+            help_type = "restructuredtext"
+            help_content = self.raw_help
+            if help_content:
+                if help_content.type == "restructuredtext":
+                    help_txt = self.help.render(
+                        static_path=self.app.url_for("/static"), host_url=self.app.url_for("/", qualified=True)
+                    )
+                    help_txt = unicodify(help_txt)
+
             tool_dict["help"] = help_txt
+            tool_dict["help_type"] = help_content.type
 
         return tool_dict
 
@@ -2570,11 +2579,15 @@ def to_json(self, trans, kwd=None, job=None, workflow_building_mode=False, histo
 
         # create tool help
         tool_help = ""
-        if self.help:
+        tool_help_type = "restructuredtext"
+        if self.raw_help and self.raw_help.type == "restructuredtext":
             tool_help = self.help.render(
                 static_path=self.app.url_for("/static"), host_url=self.app.url_for("/", qualified=True)
             )
             tool_help = unicodify(tool_help, "utf-8")
+        elif self.raw_help:
+            tool_help = self.raw_help.content
+            tool_help_type = self.raw_help.type
 
         if isinstance(self.action, tuple):
             action = self.action[0] + self.app.url_for(self.action[1])
@@ -2586,6 +2599,7 @@ def to_json(self, trans, kwd=None, job=None, workflow_building_mode=False, histo
             {
                 "id": self.id,
                 "help": tool_help,
+                "help_type": tool_help_type,
                 "citations": bool(self.citations),
                 "sharable_url": self.sharable_url,
                 "message": tool_message,
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index eeece34fe554..a74a59923114 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -1854,7 +1854,7 @@ def get_version(self):
         return self.tool.version if self.tool else self.tool_version
 
     def get_tooltip(self, static_path=None):
-        if self.tool and self.tool.help:
+        if self.tool and self.tool.raw_help and self.tool.raw_help.type == "restructuredtext":
             host_url = self.trans.url_builder("/")
             static_path = self.trans.url_builder(static_path) if static_path else ""
             return self.tool.help.render(host_url=host_url, static_path=static_path)