From ef948bccb29fec4f4a4e7bea74d69e37e56c702d Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 24 Oct 2024 08:54:44 -0400
Subject: [PATCH] Tool markdown reports.

---
 .../Dataset/DatasetAsImage/DatasetAsImage.vue |   7 +-
 .../Dataset/DatasetIndex/DatasetIndex.vue     |   3 +-
 .../Dataset/DatasetLink/DatasetLink.vue       |   3 +-
 .../History/Content/ContentItem.vue           |   6 +-
 client/src/components/Markdown/Markdown.vue   |  15 ++--
 client/src/components/Tool/ToolReport.vue     |  42 +++++++++++
 .../src/composables/datasetPathDestination.ts |   9 +--
 client/src/entry/analysis/router.js           |   6 ++
 .../config/sample/datatypes_conf.xml.sample   |   1 +
 lib/galaxy/datatypes/data.py                  |   1 +
 lib/galaxy/managers/markdown_util.py          |  66 +++++++++++++++++-
 lib/galaxy/schema/schema.py                   |   7 ++
 lib/galaxy/webapps/galaxy/api/datasets.py     |  12 ++++
 lib/galaxy/webapps/galaxy/buildapp.py         |   1 +
 .../webapps/galaxy/services/datasets.py       |  17 +++++
 .../src/components/RepositoriesForOwner.vue   |   7 +-
 test/functional/tools/data/1.bed              |  65 +++++++++++++++++
 .../functional/tools/data/rgWebLogo3_test.jpg | Bin 0 -> 21641 bytes
 .../tools/markdown_report_extra_files.xml     |  45 ++++++++++++
 .../tools/markdown_report_simple.xml          |  45 ++++++++++++
 test/functional/tools/sample_tool_conf.xml    |   2 +
 21 files changed, 341 insertions(+), 19 deletions(-)
 create mode 100644 client/src/components/Tool/ToolReport.vue
 create mode 100644 test/functional/tools/data/1.bed
 create mode 100644 test/functional/tools/data/rgWebLogo3_test.jpg
 create mode 100644 test/functional/tools/markdown_report_extra_files.xml
 create mode 100644 test/functional/tools/markdown_report_simple.xml

diff --git a/client/src/components/Dataset/DatasetAsImage/DatasetAsImage.vue b/client/src/components/Dataset/DatasetAsImage/DatasetAsImage.vue
index 5f9f2f50f39b..ff93c69d5f99 100644
--- a/client/src/components/Dataset/DatasetAsImage/DatasetAsImage.vue
+++ b/client/src/components/Dataset/DatasetAsImage/DatasetAsImage.vue
@@ -14,15 +14,14 @@ const { datasetPathDestination } = useDatasetPathDestination();
 
 const props = defineProps<Props>();
 
-const pathDestination = computed<PathDestination | null>(() =>
-    datasetPathDestination.value(props.historyDatasetId, props.path)
-);
+const pathDestination = computedAsync<PathDestination | null>(async () => {
+    return await datasetPathDestination.value(props.historyDatasetId, props.path)
+}, null);
 
 const imageUrl = computed(() => {
     if (props.path === undefined || props.path === "undefined") {
         return `${getAppRoot()}dataset/display?dataset_id=${props.historyDatasetId}`;
     }
-
     return pathDestination.value?.fileLink;
 });
 
diff --git a/client/src/components/Dataset/DatasetIndex/DatasetIndex.vue b/client/src/components/Dataset/DatasetIndex/DatasetIndex.vue
index 5001d7f2b20a..a0e2ac3514d2 100644
--- a/client/src/components/Dataset/DatasetIndex/DatasetIndex.vue
+++ b/client/src/components/Dataset/DatasetIndex/DatasetIndex.vue
@@ -1,4 +1,5 @@
 <script setup lang="ts">
+import { computedAsync } from "@vueuse/core";
 import { computed } from "vue";
 
 import type { DatasetExtraFiles } from "@/api/datasets";
@@ -13,7 +14,7 @@ const { datasetPathDestination } = useDatasetPathDestination();
 
 const props = defineProps<Props>();
 
-const pathDestination = computed<PathDestination | null>(() =>
+const pathDestination = computedAsync<PathDestination | null>(() =>
     datasetPathDestination.value(props.historyDatasetId, props.path)
 );
 
diff --git a/client/src/components/Dataset/DatasetLink/DatasetLink.vue b/client/src/components/Dataset/DatasetLink/DatasetLink.vue
index 1e9bbc33423d..ff73b85068e0 100644
--- a/client/src/components/Dataset/DatasetLink/DatasetLink.vue
+++ b/client/src/components/Dataset/DatasetLink/DatasetLink.vue
@@ -1,4 +1,5 @@
 <script setup lang="ts">
+import { computedAsync } from "@vueuse/core";
 import { computed } from "vue";
 
 import { hasDetails } from "@/api";
@@ -16,7 +17,7 @@ const { getDataset } = useDatasetStore();
 
 const props = defineProps<Props>();
 
-const pathDestination = computed<PathDestination | null>(() =>
+const pathDestination = computedAsync<PathDestination | null>(() =>
     datasetPathDestination.value(props.historyDatasetId, props.path)
 );
 
diff --git a/client/src/components/History/Content/ContentItem.vue b/client/src/components/History/Content/ContentItem.vue
index 04f3c7d0729f..d8618e52e73a 100644
--- a/client/src/components/History/Content/ContentItem.vue
+++ b/client/src/components/History/Content/ContentItem.vue
@@ -189,8 +189,12 @@ const itemUrls = computed<ItemUrls>(() => {
                     : null,
         };
     }
+    let display = `/datasets/${id}/preview`;
+    if (props.item.extension == "tool_markdown") {
+        display = `/datasets/${id}/report`;
+    }
     return {
-        display: `/datasets/${id}/preview`,
+        display: display,
         edit: `/datasets/${id}/edit`,
         showDetails: `/datasets/${id}/details`,
         reportError: `/datasets/${id}/error`,
diff --git a/client/src/components/Markdown/Markdown.vue b/client/src/components/Markdown/Markdown.vue
index 4d15b58b7e42..3b6923965c03 100644
--- a/client/src/components/Markdown/Markdown.vue
+++ b/client/src/components/Markdown/Markdown.vue
@@ -22,10 +22,10 @@
                     Edit
                     <FontAwesomeIcon icon="edit" />
                 </b-button>
-                <h1 class="float-right align-middle mr-2 mt-1 h-md">Galaxy {{ markdownConfig.model_class }}</h1>
+                <h1 v-if="title" class="float-right align-middle mr-2 mt-1 h-md">Galaxy {{ markdownConfig.model_class }}</h1>
                 <span class="float-left font-weight-light">
-                    <h1 class="text-break align-middle">
-                        Title: {{ markdownConfig.title || markdownConfig.model_class }}
+                    <h1 v-if="title" class="text-break align-middle">
+                        Title: {{ title }}
                     </h1>
                     <h2 v-if="workflowVersions" class="text-break align-middle">
                         Workflow Checkpoint: {{ workflowVersions.version }}
@@ -34,7 +34,7 @@
             </div>
             <b-badge variant="info" class="w-100 rounded mb-3 white-space-normal">
                 <div class="float-left m-1 text-break">Generated with Galaxy {{ version }} on {{ time }}</div>
-                <div class="float-right m-1">Identifier: {{ markdownConfig.id }}</div>
+                <div v-if="showIdentifier" class="float-right m-1">Identifier: {{ markdownConfig.id }}</div>
             </b-badge>
             <div>
                 <b-alert v-if="markdownErrors.length > 0" variant="warning" show>
@@ -119,6 +119,10 @@ export default {
             type: String,
             default: null,
         },
+        showIdentifier: {
+            type: Boolean,
+            default: true,
+        },
     },
     data() {
         return {
@@ -137,6 +141,9 @@ export default {
         effectiveExportLink() {
             return this.enable_beta_markdown_export ? this.exportLink : null;
         },
+        title() {
+            return this.markdownConfig.title || this.markdownConfig.model_class;
+        },
         time() {
             let generateTime = this.markdownConfig.generate_time;
             if (generateTime) {
diff --git a/client/src/components/Tool/ToolReport.vue b/client/src/components/Tool/ToolReport.vue
new file mode 100644
index 000000000000..c5bbe774f067
--- /dev/null
+++ b/client/src/components/Tool/ToolReport.vue
@@ -0,0 +1,42 @@
+<script setup lang="ts">
+import { computed, ref } from "vue";
+
+import { useConfig } from "@/composables/config";
+import { urlData } from "@/utils/url";
+
+import Markdown from "@/components/Markdown/Markdown.vue";
+
+interface Props {
+    datasetId: string;
+}
+
+const props = defineProps<Props>();
+
+const dataUrl = computed(()=> {
+    return `/api/datasets/${props.datasetId}/report`;
+});
+
+const dataRef = ref<unknown>(null);
+
+const { config, isConfigLoaded } = useConfig(true);
+
+urlData({ url: dataUrl.value }).then((data) => {
+    dataRef.value = data;
+});
+
+</script>
+
+<template>
+    <div>
+        <Markdown
+            v-if="isConfigLoaded && dataRef"
+            :markdown-config="dataRef"
+            :enable-beta-markdown-export="config.enable_beta_markdown_export"
+            download-endpoint="TODO"
+            :show-identifier="false"
+            :read-only="true" />
+        <div v-else>
+            Loading....
+        </div>
+    </div>
+</template>
diff --git a/client/src/composables/datasetPathDestination.ts b/client/src/composables/datasetPathDestination.ts
index 89f419572d1a..518f914f1cef 100644
--- a/client/src/composables/datasetPathDestination.ts
+++ b/client/src/composables/datasetPathDestination.ts
@@ -20,11 +20,11 @@ export function useDatasetPathDestination() {
     const cache = ref<{ [key: string]: PathDestinationMap }>({});
 
     const datasetPathDestination = computed(() => {
-        return (dataset_id: string, path?: string) => {
+        return async(dataset_id: string, path?: string) => {
             const targetPath = path ?? "undefined";
-            const pathDestination = cache.value[dataset_id]?.[targetPath];
+            let pathDestination = cache.value[dataset_id]?.[targetPath];
             if (!pathDestination) {
-                getPathDestination(dataset_id, path);
+                pathDestination = await getPathDestination(dataset_id, path) ?? undefined;
             }
             return pathDestination ?? null;
         };
@@ -36,7 +36,6 @@ export function useDatasetPathDestination() {
             await datasetExtraFilesStore.fetchDatasetExtFilesByDatasetId({ id: dataset_id });
             datasetExtraFiles = datasetExtraFilesStore.getDatasetExtraFiles(dataset_id);
         }
-
         if (datasetExtraFiles === null) {
             return null;
         }
@@ -66,9 +65,7 @@ export function useDatasetPathDestination() {
             }
             pathDestination.fileLink = getCompositeDatasetLink(dataset_id, datasetEntry.path);
         }
-
         set(cache.value, dataset_id, { [path]: pathDestination });
-
         return pathDestination;
     }
 
diff --git a/client/src/entry/analysis/router.js b/client/src/entry/analysis/router.js
index 011bb9ffd082..5cf4b39737c9 100644
--- a/client/src/entry/analysis/router.js
+++ b/client/src/entry/analysis/router.js
@@ -21,6 +21,7 @@ import ToolLanding from "components/Landing/ToolLanding";
 import WorkflowLanding from "components/Landing/WorkflowLanding";
 import PageDisplay from "components/PageDisplay/PageDisplay";
 import PageEditor from "components/PageEditor/PageEditor";
+import ToolReport from "components/Tool/ToolReport";
 import ToolSuccess from "components/Tool/ToolSuccess";
 import ToolsList from "components/ToolsList/ToolsList";
 import ToolsJson from "components/ToolsView/ToolsSchemaJson/ToolsJson";
@@ -239,6 +240,11 @@ export function getRouter(Galaxy) {
                             src: `/datasets/${route.params.datasetId}/display/?preview=True`,
                         }),
                     },
+                    {
+                        path: "datasets/:datasetId/report",
+                        component: ToolReport,
+                        props: true,
+                    },
                     {
                         // legacy route, potentially used by 3rd parties
                         path: "datasets/:datasetId/show_params",
diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 0e026b5a7b0a..365e722689c5 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -575,6 +575,7 @@
     <!-- End RGenetics Datatypes -->
     <datatype extension="ipynb" type="galaxy.datatypes.text:Ipynb" display_in_upload="true"/>
     <datatype extension="json" type="galaxy.datatypes.text:Json" display_in_upload="true"/>
+    <datatype extension="tool_markdown" type="galaxy.datatypes.text:Text" display_in_upload="true"/>
     <datatype extension="expression.json" type="galaxy.datatypes.text:ExpressionJson" display_in_upload="true"/>
     <!-- graph datatypes -->
     <datatype extension="xgmml" type="galaxy.datatypes.graph:Xgmml" display_in_upload="true"/>
diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index 0024adea6155..23503e6c2358 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -465,6 +465,7 @@ def _serve_file_download(self, headers, data, trans, to_ext, file_size, **kwd):
         composite_extensions = trans.app.datatypes_registry.get_composite_extensions()
         composite_extensions.append("html")  # for archiving composite datatypes
         composite_extensions.append("data_manager_json")  # for downloading bundles if bundled.
+        composite_extensions.append("tool_markdown")
 
         if data.extension in composite_extensions:
             return self._archive_composite_dataset(trans, data, headers, do_action=kwd.get("do_action", "zip"))
diff --git a/lib/galaxy/managers/markdown_util.py b/lib/galaxy/managers/markdown_util.py
index 02545399e997..757a9980e2cc 100644
--- a/lib/galaxy/managers/markdown_util.py
+++ b/lib/galaxy/managers/markdown_util.py
@@ -900,7 +900,7 @@ def _remap(container, line):
             )
         if container == "history_link":
             return (f"history_link(history_id={invocation.history.id})\n", False)
-        if container == "invocation_time":
+        elif container == "invocation_time":
             return (f"invocation_time(invocation_id={invocation.id})\n", False)
         ref_object_type = None
         output_match = re.search(OUTPUT_LABEL_PATTERN, line)
@@ -953,6 +953,70 @@ def find_non_empty_group(match):
     return galaxy_markdown
 
 
+def resolve_job_markdown(trans, job, job_markdown):
+    """Resolve job objects to convert tool markdown to 'internal' representation.
+
+    Replace references to abstract workflow parts with actual galaxy object IDs corresponding
+    to the actual executed workflow. For instance:
+
+        convert output=name -to- history_dataset_id=<id> | history_dataset_collection_id=<id>
+        convert input=name -to- history_dataset_id=<id> | history_dataset_collection_id=<id>
+        convert argument-less job directives to job
+    """
+    io_dicts = job.io_dicts()
+
+    def _remap(container, line):
+        if container == "history_link":
+            return (f"history_link(history_id={job.history.id})\n", False)
+        elif container == "tool_stdout":
+            return (f"tool_stdout(job_id={job.id})\n", False)
+        elif container == "tool_stderr":
+            return (f"tool_stderr(job_id={job.id})\n", False)
+        elif container == "job_parameters":
+            return (f"job_parameters(job_id={job.id})\n", False)
+        elif container == "job_metrics":
+            return (f"job_metrics(job_id={job.id})\n", False)
+        ref_object_type = None
+        output_match = re.search(OUTPUT_LABEL_PATTERN, line)
+        input_match = re.search(INPUT_LABEL_PATTERN, line)
+
+        def find_non_empty_group(match):
+            for group in match.groups():
+                if group:
+                    return group
+
+        target_match: Optional[Match]
+        ref_object: Optional[Any]
+        if output_match:
+            target_match = output_match
+            name = find_non_empty_group(target_match)
+            if name in io_dicts.out_data:
+                ref_object = io_dicts.out_data[name]
+            elif name in io_dicts.out_collections:
+                ref_object = io_dicts.out_collections[name]
+            else:
+                raise Exception("Unknown exception")
+        elif input_match:
+            target_match = input_match
+            name = find_non_empty_group(target_match)
+            ref_object = io_dicts.inp_data[name]
+        else:
+            target_match = None
+            ref_object = None
+        if ref_object:
+            assert target_match  # tell type system, this is set when ref_object is set
+            if ref_object_type is None:
+                if ref_object.history_content_type == "dataset":
+                    ref_object_type = "history_dataset"
+                else:
+                    ref_object_type = "history_dataset_collection"
+            line = line.replace(target_match.group(), f"{ref_object_type}_id={ref_object.id}")
+        return (line, False)
+
+    galaxy_markdown = _remap_galaxy_markdown_calls(_remap, job_markdown)
+    return galaxy_markdown
+
+
 def _remap_galaxy_markdown_containers(func, markdown):
     new_markdown = markdown
 
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index 0d9646316e59..4bd05d09753e 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -3846,6 +3846,13 @@ class PageDetails(PageSummary):
     model_config = ConfigDict(extra="allow")
 
 
+class ToolReportForDataset(BaseModel):
+    content: Optional[str] = ContentField
+    generate_version: Optional[str] = GenerateVersionField
+    generate_time: Optional[str] = GenerateTimeField
+    model_config = ConfigDict(extra="allow")
+
+
 class PageSummaryList(RootModel):
     root: List[PageSummary] = Field(
         default=[],
diff --git a/lib/galaxy/webapps/galaxy/api/datasets.py b/lib/galaxy/webapps/galaxy/api/datasets.py
index eba6795100fd..a7dbf8130550 100644
--- a/lib/galaxy/webapps/galaxy/api/datasets.py
+++ b/lib/galaxy/webapps/galaxy/api/datasets.py
@@ -39,6 +39,7 @@
     AsyncTaskResultSummary,
     DatasetAssociationRoles,
     DatasetSourceType,
+    ToolReportForDataset,
 )
 from galaxy.util.zipstream import ZipstreamWrapper
 from galaxy.webapps.base.api import GalaxyFileResponse
@@ -503,6 +504,17 @@ def compute_hash(
     ) -> AsyncTaskResultSummary:
         return self.service.compute_hash(trans, dataset_id, payload, hda_ldda=hda_ldda)
 
+    @router.get(
+        "/api/datasets/{dataset_id}/report",
+        summary="Return JSON content Galaxy will use to render Markdown reports",
+    )
+    def report(
+        self,
+        dataset_id: HistoryDatasetIDPathParam,
+        trans=DependsOnTrans,
+    ) -> ToolReportForDataset:
+        return self.service.report(trans, dataset_id)
+
     @router.put(
         "/api/datasets/{dataset_id}/object_store_id",
         summary="Update an object store ID for a dataset you own.",
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index e1897420f9a5..8ffce93080c7 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -280,6 +280,7 @@ def app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs):
     webapp.add_client_route("/datasets/{dataset_id}/error")
     webapp.add_client_route("/datasets/{dataset_id}/details")
     webapp.add_client_route("/datasets/{dataset_id}/preview")
+    webapp.add_client_route("/datasets/{dataset_id}/report")
     webapp.add_client_route("/datasets/{dataset_id}/show_params")
     webapp.add_client_route("/collection/{collection_id}/edit")
     webapp.add_client_route("/jobs/submission/success")
diff --git a/lib/galaxy/webapps/galaxy/services/datasets.py b/lib/galaxy/webapps/galaxy/services/datasets.py
index 4f6fef304697..d9cca09144b6 100644
--- a/lib/galaxy/webapps/galaxy/services/datasets.py
+++ b/lib/galaxy/webapps/galaxy/services/datasets.py
@@ -47,6 +47,10 @@
     HistoryContentsManager,
 )
 from galaxy.managers.lddas import LDDAManager
+from galaxy.managers.markdown_util import (
+    ready_galaxy_markdown_for_export,
+    resolve_job_markdown,
+)
 from galaxy.model.base import transaction
 from galaxy.objectstore.badges import BadgeDict
 from galaxy.schema import (
@@ -70,6 +74,7 @@
     DatasetSourceType,
     EncodedDatasetSourceId,
     Model,
+    ToolReportForDataset,
     UpdateDatasetPermissionsPayload,
 )
 from galaxy.schema.tasks import ComputeDatasetHashTaskRequest
@@ -506,6 +511,18 @@ def compute_hash(
         result = compute_dataset_hash.delay(request=request, task_user_id=getattr(trans.user, "id", None))
         return async_task_summary(result)
 
+    def report(self, trans: ProvidesHistoryContext, dataset_id: DecodedDatabaseIdField) -> ToolReportForDataset:
+        dataset_instance = self.hda_manager.get_accessible(dataset_id, trans.user)
+        self.hda_manager.ensure_dataset_on_disk(trans, dataset_instance)
+        file_path = trans.app.object_store.get_filename(dataset_instance.dataset)
+        raw_content = open(file_path).read()
+        internal_markdown = resolve_job_markdown(trans, dataset_instance.creating_job, raw_content)
+        content, extra_attributes = ready_galaxy_markdown_for_export(trans, internal_markdown)
+        return ToolReportForDataset(
+            content=content,
+            **extra_attributes,
+        )
+
     def drs_dataset_instance(self, object_id: str) -> Tuple[int, DatasetSourceType]:
         if object_id.startswith("hda-"):
             decoded_object_id = self.decode_id(object_id[len("hda-") :], kind="drs")
diff --git a/lib/tool_shed/webapp/frontend/src/components/RepositoriesForOwner.vue b/lib/tool_shed/webapp/frontend/src/components/RepositoriesForOwner.vue
index 5db3578ca516..e0e44042cd58 100644
--- a/lib/tool_shed/webapp/frontend/src/components/RepositoriesForOwner.vue
+++ b/lib/tool_shed/webapp/frontend/src/components/RepositoriesForOwner.vue
@@ -48,5 +48,10 @@ const rows = computed(() => {
 <template>
     <loading-div v-if="loading" />
     <error-banner error="Failed to load repositories" v-else-if="error"> </error-banner>
-    <repositories-grid :title="`Repositories for ${username}`" :rows="rows" :on-scroll="onScroll" />
+    <repositories-grid
+        :title="`Repositories for ${username}`"
+        :rows="rows"
+        :on-scroll="onScroll"
+        :allow-search="true"
+    />
 </template>
diff --git a/test/functional/tools/data/1.bed b/test/functional/tools/data/1.bed
new file mode 100644
index 000000000000..eb4c30e347a1
--- /dev/null
+++ b/test/functional/tools/data/1.bed
@@ -0,0 +1,65 @@
+chr1	147962192	147962580	CCDS989.1_cds_0_0_chr1_147962193_r	0	-
+chr1	147984545	147984630	CCDS990.1_cds_0_0_chr1_147984546_f	0	+
+chr1	148078400	148078582	CCDS993.1_cds_0_0_chr1_148078401_r	0	-
+chr1	148185136	148185276	CCDS996.1_cds_0_0_chr1_148185137_f	0	+
+chr10	55251623	55253124	CCDS7248.1_cds_0_0_chr10_55251624_r	0	-
+chr11	116124407	116124501	CCDS8374.1_cds_0_0_chr11_116124408_r	0	-
+chr11	116206508	116206563	CCDS8377.1_cds_0_0_chr11_116206509_f	0	+
+chr11	116211733	116212337	CCDS8378.1_cds_0_0_chr11_116211734_r	0	-
+chr11	1812377	1812407	CCDS7726.1_cds_0_0_chr11_1812378_f	0	+
+chr12	38440094	38440321	CCDS8736.1_cds_0_0_chr12_38440095_r	0	-
+chr13	112381694	112381953	CCDS9526.1_cds_0_0_chr13_112381695_f	0	+
+chr14	98710240	98712285	CCDS9949.1_cds_0_0_chr14_98710241_r	0	-
+chr15	41486872	41487060	CCDS10096.1_cds_0_0_chr15_41486873_r	0	-
+chr15	41673708	41673857	CCDS10097.1_cds_0_0_chr15_41673709_f	0	+
+chr15	41679161	41679250	CCDS10098.1_cds_0_0_chr15_41679162_r	0	-
+chr15	41826029	41826196	CCDS10101.1_cds_0_0_chr15_41826030_f	0	+
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+chr16	244413	244681	CCDS10402.1_cds_0_0_chr16_244414_f	0	+
+chr16	259268	259383	CCDS10403.1_cds_0_0_chr16_259269_r	0	-
+chr18	23786114	23786321	CCDS11891.1_cds_0_0_chr18_23786115_r	0	-
+chr18	59406881	59407046	CCDS11985.1_cds_0_0_chr18_59406882_f	0	+
+chr18	59455932	59456337	CCDS11986.1_cds_0_0_chr18_59455933_r	0	-
+chr18	59600586	59600754	CCDS11988.1_cds_0_0_chr18_59600587_f	0	+
+chr19	59068595	59069564	CCDS12866.1_cds_0_0_chr19_59068596_f	0	+
+chr19	59236026	59236146	CCDS12872.1_cds_0_0_chr19_59236027_r	0	-
+chr19	59297998	59298008	CCDS12877.1_cds_0_0_chr19_59297999_f	0	+
+chr19	59302168	59302288	CCDS12878.1_cds_0_0_chr19_59302169_r	0	-
+chr2	118288583	118288668	CCDS2120.1_cds_0_0_chr2_118288584_f	0	+
+chr2	118394148	118394202	CCDS2121.1_cds_0_0_chr2_118394149_r	0	-
+chr2	220190202	220190242	CCDS2441.1_cds_0_0_chr2_220190203_f	0	+
+chr2	220229609	220230869	CCDS2443.1_cds_0_0_chr2_220229610_r	0	-
+chr20	33330413	33330423	CCDS13249.1_cds_0_0_chr20_33330414_r	0	-
+chr20	33513606	33513792	CCDS13255.1_cds_0_0_chr20_33513607_f	0	+
+chr20	33579500	33579527	CCDS13256.1_cds_0_0_chr20_33579501_r	0	-
+chr20	33593260	33593348	CCDS13257.1_cds_0_0_chr20_33593261_f	0	+
+chr21	32707032	32707192	CCDS13614.1_cds_0_0_chr21_32707033_f	0	+
+chr21	32869641	32870022	CCDS13615.1_cds_0_0_chr21_32869642_r	0	-
+chr21	33321040	33322012	CCDS13620.1_cds_0_0_chr21_33321041_f	0	+
+chr21	33744994	33745040	CCDS13625.1_cds_0_0_chr21_33744995_r	0	-
+chr22	30120223	30120265	CCDS13897.1_cds_0_0_chr22_30120224_f	0	+
+chr22	30160419	30160661	CCDS13898.1_cds_0_0_chr22_30160420_r	0	-
+chr22	30665273	30665360	CCDS13901.1_cds_0_0_chr22_30665274_f	0	+
+chr22	30939054	30939266	CCDS13903.1_cds_0_0_chr22_30939055_r	0	-
+chr5	131424298	131424460	CCDS4149.1_cds_0_0_chr5_131424299_f	0	+
+chr5	131556601	131556672	CCDS4151.1_cds_0_0_chr5_131556602_r	0	-
+chr5	131621326	131621419	CCDS4152.1_cds_0_0_chr5_131621327_f	0	+
+chr5	131847541	131847666	CCDS4155.1_cds_0_0_chr5_131847542_r	0	-
+chr6	108299600	108299744	CCDS5061.1_cds_0_0_chr6_108299601_r	0	-
+chr6	108594662	108594687	CCDS5063.1_cds_0_0_chr6_108594663_f	0	+
+chr6	108640045	108640151	CCDS5064.1_cds_0_0_chr6_108640046_r	0	-
+chr6	108722976	108723115	CCDS5067.1_cds_0_0_chr6_108722977_f	0	+
+chr7	113660517	113660685	CCDS5760.1_cds_0_0_chr7_113660518_f	0	+
+chr7	116512159	116512389	CCDS5771.1_cds_0_0_chr7_116512160_r	0	-
+chr7	116714099	116714152	CCDS5773.1_cds_0_0_chr7_116714100_f	0	+
+chr7	116945541	116945787	CCDS5774.1_cds_0_0_chr7_116945542_r	0	-
+chr8	118881131	118881317	CCDS6324.1_cds_0_0_chr8_118881132_r	0	-
+chr9	128764156	128764189	CCDS6914.1_cds_0_0_chr9_128764157_f	0	+
+chr9	128787519	128789136	CCDS6915.1_cds_0_0_chr9_128787520_r	0	-
+chr9	128882427	128882523	CCDS6917.1_cds_0_0_chr9_128882428_f	0	+
+chr9	128937229	128937445	CCDS6919.1_cds_0_0_chr9_128937230_r	0	-
+chrX	122745047	122745924	CCDS14606.1_cds_0_0_chrX_122745048_f	0	+
+chrX	152648964	152649196	CCDS14733.1_cds_0_0_chrX_152648965_r	0	-
+chrX	152691446	152691471	CCDS14735.1_cds_0_0_chrX_152691447_f	0	+
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diff --git a/test/functional/tools/data/rgWebLogo3_test.jpg b/test/functional/tools/data/rgWebLogo3_test.jpg
new file mode 100644
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HcmV?d00001

diff --git a/test/functional/tools/markdown_report_extra_files.xml b/test/functional/tools/markdown_report_extra_files.xml
new file mode 100644
index 000000000000..d59ffcc59fc2
--- /dev/null
+++ b/test/functional/tools/markdown_report_extra_files.xml
@@ -0,0 +1,45 @@
+<tool id="markdown_report_extra_files" name="markdown_report_extra_files" version="1.0">
+    <command><![CDATA[
+        mkdir '$output_report.extra_files_path';
+        cp '$__tool_directory__/data/1.bed' > '$output_report.extra_files_path/test.bed';
+        cp '$__tool_directory__/data/rgWebLogo3_test.jpg' '$output_report.extra_files_path/rgWebLogo3_test.jpg';
+        echo "I am writing this to standard output!";
+        cp '${tool_markdown}' '${output_report}';
+    ]]></command>
+    <configfiles>
+        <configfile name="tool_markdown"><![CDATA[
+# ${title}
+
+Here is an image we just stuck in an extra files path
+
+```galaxy
+history_dataset_as_image(output=output_report, path="rgWebLogo3_test.jpg")
+```
+
+This doesn't work yet - need to implement path on this directive type.
+
+```galaxy
+history_dataset_as_table(output=output_report, path="test.bed")
+```
+
+The standard out for this tool execution is:
+
+```galaxy
+tool_stdout()
+```
+
+This is my document and I have populated the title from a parameter.
+]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="title" type="text" label="Title"/>
+    </inputs>
+    <outputs>
+        <!-- <data name="output_directory" format="html"/> -->
+        <data name="output_report" format="tool_markdown"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+    </help>
+</tool>
diff --git a/test/functional/tools/markdown_report_simple.xml b/test/functional/tools/markdown_report_simple.xml
new file mode 100644
index 000000000000..cc714558754e
--- /dev/null
+++ b/test/functional/tools/markdown_report_simple.xml
@@ -0,0 +1,45 @@
+<tool id="markdown_report_simple" name="markdown_report_simple" version="1.0">
+    <command><![CDATA[
+        echo "Some contents for standard output";
+        echo "Hello World" > '$output_text';
+        cp '$__tool_directory__/data/1.bed' '$output_table';
+        cp '${tool_markdown}' '${output_report}';
+    ]]></command>
+    <configfiles>
+        <configfile name="tool_markdown"><![CDATA[
+# ${title}
+
+Here is a peek of the exciting stuff we did:
+
+```galaxy
+history_dataset_peek(output=output_text)
+```
+
+We also produced a table
+
+```galaxy
+history_dataset_as_table(output=output_table, header="Table Header", footer="A description of the table", compact=true)
+```
+
+The standard output for this tool execution is:
+
+```galaxy
+tool_stdout()
+```
+
+This is my document and I have populated the title from a parameter.
+]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="title" type="text" label="Title"/>
+    </inputs>
+    <outputs>
+        <data name="output_text" format="txt"/>
+        <data name="output_table" format="tsv"/>
+        <data name="output_report" format="tool_markdown"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+    </help>
+</tool>
diff --git a/test/functional/tools/sample_tool_conf.xml b/test/functional/tools/sample_tool_conf.xml
index bb9d7568f600..498d768a498b 100644
--- a/test/functional/tools/sample_tool_conf.xml
+++ b/test/functional/tools/sample_tool_conf.xml
@@ -232,6 +232,8 @@
   <tool file="text_repeat.xml" />
   <tool file="integer_default.xml" />
   <tool file="all_output_types.xml" />
+  <tool file="markdown_report_simple.xml" />
+  <tool file="markdown_report_extra_files.xml" />
   <tool file="multiple_versions_v01.xml" />
   <tool file="multiple_versions_v01galaxy6.xml" />
   <tool file="multiple_versions_v02.xml" />