Skip mako for rendering tool help

Fixes

```
Traceback (most recent call last):
  File "galaxy/web/framework/decorators.py", line 340, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "galaxy/webapps/galaxy/api/tools.py", line 446, in build
    return tool.to_json(trans, kwd.get("inputs", kwd), history=history)
  File "galaxy/tools/__init__.py", line 2945, in to_json
    tool_help = self.help.render(
  File "mako/template.py", line 434, in render
    return runtime._render(self, self.callable_, args, data)
  File "mako/runtime.py", line 874, in _render
    _render_context(
  File "mako/runtime.py", line 916, in _render_context
    _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
  File "mako/runtime.py", line 943, in _exec_template
    callable_(context, *args, **kwargs)
  File "memory:0x7fd82e70d0f0", line 22, in render_body
AttributeError: 'Undefined' object has no attribute 'name'
```
for https://github.com/galaxyproject/tools-iuc/blob/main/tools/teloscope/teloscope.xml#L220

lib/galaxy/tools/__init__.py

@@ -25,7 +25,6 @@ from urllib.parse import unquote_plus
 from uuid import UUID
 
 import webob.exc
-from mako.template import Template
 from packaging.version import Version
 from sqlalchemy import (
     delete,
@@ -999,7 +998,6 @@ class Tool(UsesDictVisibleKeys, ToolParameterBundle):
     tool_action: ToolAction
     tool_type_local = False
     dict_collection_visible_keys = ["id", "name", "version", "description", "labels"]
-    __help: Optional[Template]
     job_search: "JobSearch"
     version: str
 
@@ -1080,7 +1078,6 @@ class Tool(UsesDictVisibleKeys, ToolParameterBundle):
         self.javascript_requirements: Optional[list[JavascriptRequirement]] = None
         self.credentials: Optional[list[CredentialsRequirement]] = None
         self._is_workflow_compatible = None
-        self.__help = None
         self.__tests: Optional[str] = None
         try:
             self.parse(tool_source, guid=guid, dynamic=dynamic)
@@ -1947,20 +1944,24 @@ class Tool(UsesDictVisibleKeys, ToolParameterBundle):
             )
 
     @property
-    def help(self) -> Template:
+    def help_html(self) -> str:
+        """Returns the help content converted from RST to HTML (without variable substitution)."""
         help_content = self.raw_help
         assert help_content
         assert help_content.format == "restructuredtext"
         try:
-            return Template(
-                rst_to_html(help_content.content),
-                input_encoding="utf-8",
-                default_filters=["decode.utf8"],
-                encoding_errors="replace",
-            )
+            return rst_to_html(help_content.content)
         except Exception:
             log.info("Exception while parsing help for tool with id '%s'", self.id)
-            return Template("", input_encoding="utf-8")
+            return ""
+
+    def render_help(self, static_path: str, host_url: str) -> str:
+        """Renders the help HTML with variable substitution for static_path and host_url."""
+        help_html = self.help_html
+        # Replace Mako-style variables with actual values
+        help_html = help_html.replace("${static_path}", static_path)
+        help_html = help_html.replace("${host_url}", host_url)
+        return help_html
 
     @property
     def biotools_reference(self) -> Optional[str]:
@@ -2707,8 +2708,8 @@ class Tool(UsesDictVisibleKeys, ToolParameterBundle):
         # Retrieve tool help images and rewrite the tool's xml into a temporary file with the path
         # modified to be relative to the repository root.
         image_found = False
-        if self.help is not None:
-            tool_help = self.help._source
+        if self.raw_help is not None and self.raw_help.format == "restructuredtext":
+            tool_help = self.help_html
             # Check each line of the rendered tool help for an image tag that points to a location under static/
             for help_line in tool_help.split("\n"):
                 image_regex = re.compile(r'img alt="[^"]+" src="\${static_path}/([^"]+)"')
@@ -2866,10 +2867,9 @@ class Tool(UsesDictVisibleKeys, ToolParameterBundle):
             if help_content:
                 help_format = help_content.format
                 if help_format == "restructuredtext":
-                    help_txt = self.help.render(
+                    help_txt = self.render_help(
                         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_format"] = help_format
@@ -2942,10 +2942,9 @@ class Tool(UsesDictVisibleKeys, ToolParameterBundle):
         tool_help = ""
         tool_help_format = "restructuredtext"
         if self.raw_help and self.raw_help.format == "restructuredtext":
-            tool_help = self.help.render(
+            tool_help = self.render_help(
                 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_format = self.raw_help.format

lib/galaxy/workflow/modules.py

@@ -2065,7 +2065,7 @@ class ToolModule(WorkflowModule):
         if self.tool and self.tool.raw_help and self.tool.raw_help.format == "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)
+            return self.tool.render_help(host_url=host_url, static_path=static_path)
 
     # ---- Configuration time -----------------------------------------------
 

lib/tool_shed/webapp/templates/webapps/tool_shed/repository/tool_form.mako

@@ -106,20 +106,14 @@
                     </form>
                 </div>
             </div>
-            %if tool.help:
-                <div class="toolHelp">
-                    <div class="toolHelpBody">
-                        <%
-                            tool_help = tool.help
-                            # Help is Mako template, so render using current static path.
-                            tool_help = tool_help.render( static_path=h.url_for( '/static' ) )
-                            # Convert to unicode to display non-ascii characters.
-                            tool_help = util.unicodify( tool_help, 'utf-8')
-                        %>
-                        ${tool_help}
-                    </div>
+            <div class="toolHelp">
+                <div class="toolHelpBody">
+                    <%
+                        tool_help = tool.render_help( host_url=h.url_for( '/' ), static_path=h.url_for( '/static' ) )
+                    %>
+                    ${tool_help}
                 </div>
-            %endif
+            </div>
         %else:
             Tool not properly loaded.
         %endif