diff --git a/planemo/autoupdate.py b/planemo/autoupdate.py
index 2d139ab98..1a9324d6b 100644
--- a/planemo/autoupdate.py
+++ b/planemo/autoupdate.py
@@ -4,7 +4,6 @@
 import itertools
 import re
 import xml.etree.ElementTree as ET
-from string import Template
 from typing import (
     Any,
     DefaultDict,
@@ -26,7 +25,8 @@
 
 import planemo.conda
 from planemo.galaxy.workflows import (
-    guess_tool_shed_url,
+    get_tool_ids_for_workflow,
+    get_toolshed_url_for_tool_id,
     MAIN_TOOLSHED_URL,
 )
 from planemo.io import (
@@ -294,14 +294,6 @@ def get_newest_tool_id(tool_ids: List[str]) -> str:
     )[-1]
 
 
-def get_toolshed_url_for_tool_id(tool_id: str) -> Optional[str]:
-    components = tool_id.split("/repos")
-    if len(components) > 1:
-        tool_shed_fqdn = components[0]
-        return guess_tool_shed_url(tool_shed_fqdn=tool_shed_fqdn)
-    return None
-
-
 def outdated_tools(  # noqa: C901
     ctx: "PlanemoCliContext", wf_dict: Dict[str, Any], tools_to_skip: List[str]
 ) -> Dict[str, Dict[str, str]]:
@@ -355,22 +347,6 @@ def outdated_tools_rec(wf_dict: Dict[str, Any]) -> None:
     return outdated_tool_dict
 
 
-def get_tool_ids_for_workflow(wf_dict: Dict[str, Any], tool_ids: Optional[List[str]] = None) -> List[str]:
-    tool_ids = [] if tool_ids is None else tool_ids
-    steps = wf_dict["steps"].values() if isinstance(wf_dict["steps"], dict) else wf_dict["steps"]
-    for step in steps:
-        if step.get("type", "tool") == "tool" and not step.get("run", {}).get("class") == "GalaxyWorkflow":
-            tool_id = step["tool_id"]
-            tool_ids.append(tool_id)
-        elif step.get("type") == "subworkflow":  # GA SWF
-            get_tool_ids_for_workflow(step["subworkflow"], tool_ids=tool_ids)
-        elif step.get("run", {}).get("class") == "GalaxyWorkflow":  # gxformat2 SWF
-            get_tool_ids_for_workflow(step["run"], tool_ids=tool_ids)
-        else:
-            continue
-    return list(dict.fromkeys(tool_ids))
-
-
 def get_tools_to_update(
     ctx: "PlanemoCliContext", workflow: "Runnable", tools_to_skip: List[str]
 ) -> Dict[str, Dict[str, str]]:
@@ -383,18 +359,6 @@ def get_tools_to_update(
     return outdated_tools(ctx, wf_dict, tools_to_skip)
 
 
-def get_shed_tools_conf_string_for_tool_ids(tool_ids: List[str]) -> str:
-    tool_shed_urls = set(get_toolshed_url_for_tool_id(tool_id) for tool_id in tool_ids if tool_id)
-    cleaned_tool_shed_urls = set(_ for _ in tool_shed_urls if _ is not None)
-    TOOL_SHEDS_CONF_TEMPLATE = Template("""<tool_sheds>${tool_shed_lines}</tool_sheds>""")
-    tool_sheds: List[str] = []
-    # sort tool_shed_urls from shortest to longest, as https://github.com/galaxyproject/galaxy/blob/c7cb47a1b18ccd5b39075a705bbd2f34572755fe/lib/galaxy/util/tool_shed/tool_shed_registry.py#L106-L118
-    # has a bug where a toolshed that is an exact substring of another registered toolshed would wrongly be selected.
-    for tool_shed_url in sorted(cleaned_tool_shed_urls, key=lambda url: len(url)):
-        tool_sheds.append(f'<tool_shed name="{tool_shed_url.split("://")[-1]}" url="{tool_shed_url}" />')
-    return TOOL_SHEDS_CONF_TEMPLATE.substitute(tool_shed_lines="".join(tool_sheds))
-
-
 def autoupdate_wf(ctx: "PlanemoCliContext", config: "LocalGalaxyConfig", wf: "Runnable") -> Dict[str, Any]:
     workflow_id = config.workflow_id_for_runnable(wf)
     _update_wf(config, workflow_id)
diff --git a/planemo/commands/cmd_autoupdate.py b/planemo/commands/cmd_autoupdate.py
index 464702b70..40c988810 100644
--- a/planemo/commands/cmd_autoupdate.py
+++ b/planemo/commands/cmd_autoupdate.py
@@ -135,14 +135,6 @@ def cli(ctx, paths, **kwds):  # noqa C901
             kwds["install_repository_dependencies"] = False
             kwds["shed_install"] = True
 
-        tool_ids = []
-        for workflow in modified_workflows:
-            with open(workflow.path) as fh:
-                wf_dict = yaml.safe_load(fh)
-                tool_ids.extend(autoupdate.get_tool_ids_for_workflow(wf_dict=wf_dict))
-        tool_ids = list(dict.fromkeys(tool_ids))
-        kwds["tool_sheds_config_content"] = autoupdate.get_shed_tools_conf_string_for_tool_ids(tool_ids)
-
         with engine_context(ctx, **kwds) as galaxy_engine:
             with galaxy_engine.ensure_runnables_served(modified_workflows) as config:
                 for workflow in modified_workflows:
diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py
index ec7c13409..c23ec429e 100644
--- a/planemo/galaxy/config.py
+++ b/planemo/galaxy/config.py
@@ -35,7 +35,10 @@
 from planemo.config import OptionSource
 from planemo.deps import ensure_dependency_resolvers_conf_configured
 from planemo.docker import docker_host_args
-from planemo.galaxy.workflows import remote_runnable_to_workflow_id
+from planemo.galaxy.workflows import (
+    get_toolshed_url_for_tool_id,
+    remote_runnable_to_workflow_id,
+)
 from planemo.io import (
     communicate,
     kill_pid_file,
@@ -48,6 +51,10 @@
     write_file,
 )
 from planemo.mulled import build_involucro_context
+from planemo.runnable import (
+    Runnable,
+    RunnableType,
+)
 from planemo.shed import tool_shed_url
 from .api import (
     DEFAULT_ADMIN_API_KEY,
@@ -258,6 +265,10 @@ def config_join(*args):
         shed_tool_path = kwds.get("shed_tool_path") or config_join("shed_tools")
         _ensure_directory(shed_tool_path)
 
+        # Find tool sheds to add to config
+        tool_sheds_config_content = get_tool_sheds_conf_for_runnables(runnables)
+        if tool_sheds_config_content:
+            kwds["tool_sheds_config_content"] = tool_sheds_config_content
         sheds_config_path = _configure_sheds_config_file(ctx, config_directory, **kwds)
         port = _get_port(kwds)
         properties = _shared_galaxy_properties(config_directory, kwds, for_tests=for_tests)
@@ -326,6 +337,7 @@ def local_galaxy_config(ctx, runnables, for_tests=False, **kwds):
     test_data_dir = _find_test_data(runnables, **kwds)
     tool_data_tables = _find_tool_data_table(runnables, test_data_dir=test_data_dir, **kwds)
     data_manager_config_paths = [r.data_manager_conf_path for r in runnables if r.data_manager_conf_path]
+
     galaxy_root = _find_galaxy_root(ctx, **kwds)
     install_galaxy = kwds.get("install_galaxy", False)
     if galaxy_root is not None:
@@ -389,6 +401,10 @@ def config_join(*args):
         shed_tool_path = kwds.get("shed_tool_path") or config_join("shed_tools")
         _ensure_directory(shed_tool_path)
 
+        # Find tool sheds to add to config
+        tool_sheds_config_content = get_tool_sheds_conf_for_runnables(runnables)
+        if tool_sheds_config_content:
+            kwds["tool_sheds_config_content"] = tool_sheds_config_content
         sheds_config_path = _configure_sheds_config_file(ctx, config_directory, **kwds)
 
         database_location = config_join("galaxy.sqlite")
@@ -568,19 +584,27 @@ def _all_tool_paths(
     all_tool_paths = {r.path for r in runnables if r.has_tools and not r.data_manager_conf_path}
     extra_tools = _expand_paths(galaxy_root, extra_tools=extra_tools)
     all_tool_paths.update(extra_tools)
-    for runnable in runnables:
-        if runnable.type.name == "galaxy_workflow":
-            tool_ids = find_tool_ids(runnable.path)
-            for tool_id in tool_ids:
-                tool_paths = DISTRO_TOOLS_ID_TO_PATH.get(tool_id)
-                if tool_paths:
-                    if isinstance(tool_paths, str):
-                        tool_paths = [tool_paths]
-                    all_tool_paths.update(tool_paths)
+    for tool_id in get_tool_ids_for_runnables(runnables):
+        tool_paths = DISTRO_TOOLS_ID_TO_PATH.get(tool_id)
+        if tool_paths:
+            if isinstance(tool_paths, str):
+                tool_paths = [tool_paths]
+            all_tool_paths.update(tool_paths)
 
     return all_tool_paths
 
 
+def get_workflow_runnables(runnables: List[Runnable]) -> List[Runnable]:
+    return [r for r in runnables if r.type == RunnableType.galaxy_workflow and r.has_path]
+
+
+def get_tool_ids_for_runnables(runnables) -> List[str]:
+    tool_ids = []
+    for r in get_workflow_runnables(runnables):
+        tool_ids.extend(find_tool_ids(r.path))
+    return list(dict.fromkeys(tool_ids))
+
+
 def _shared_galaxy_properties(config_directory, kwds, for_tests):
     """Setup properties useful for local and Docker Galaxy instances.
 
@@ -1201,6 +1225,27 @@ def _search_tool_path_for(path, target, extra_paths=None):
     return None
 
 
+def get_tool_sheds_conf_for_runnables(runnables: Optional[List[Runnable]]) -> Optional[str]:
+    if runnables:
+        tool_ids = get_tool_ids_for_runnables(runnables)
+        return get_shed_tools_conf_string_for_tool_ids(tool_ids)
+    return None
+
+
+def get_shed_tools_conf_string_for_tool_ids(tool_ids: List[str]) -> str:
+    tool_shed_urls = set(get_toolshed_url_for_tool_id(tool_id) for tool_id in tool_ids if tool_id)
+    # always add main toolshed
+    tool_shed_urls.add("https://toolshed.g2.bx.psu.edu/")
+    cleaned_tool_shed_urls = set(_ for _ in tool_shed_urls if _ is not None)
+    TOOL_SHEDS_CONF_TEMPLATE = Template("""<tool_sheds>${tool_shed_lines}</tool_sheds>""")
+    tool_sheds: List[str] = []
+    # sort tool_shed_urls from shortest to longest, as https://github.com/galaxyproject/galaxy/blob/c7cb47a1b18ccd5b39075a705bbd2f34572755fe/lib/galaxy/util/tool_shed/tool_shed_registry.py#L106-L118
+    # has a bug where a toolshed that is an exact substring of another registered toolshed would wrongly be selected.
+    for shed_url in sorted(cleaned_tool_shed_urls, key=lambda url: len(url)):
+        tool_sheds.append(f'<tool_shed name="{shed_url.split("://")[-1]}" url="{shed_url}" />')
+    return TOOL_SHEDS_CONF_TEMPLATE.substitute(tool_shed_lines="".join(tool_sheds))
+
+
 def _configure_sheds_config_file(ctx, config_directory, **kwds):
     contents = kwds.get("tool_sheds_config_content")
     if not contents:
diff --git a/planemo/galaxy/workflows.py b/planemo/galaxy/workflows.py
index 9ad6e9abb..48ee9d135 100644
--- a/planemo/galaxy/workflows.py
+++ b/planemo/galaxy/workflows.py
@@ -61,6 +61,14 @@ def guess_tool_shed_url(tool_shed_fqdn: str) -> Optional[str]:
     return None
 
 
+def get_toolshed_url_for_tool_id(tool_id: str) -> Optional[str]:
+    components = tool_id.split("/repos")
+    if len(components) > 1:
+        tool_shed_fqdn = components[0]
+        return guess_tool_shed_url(tool_shed_fqdn=tool_shed_fqdn)
+    return None
+
+
 def load_shed_repos(runnable):
     if runnable.type.name != "galaxy_workflow":
         return []
@@ -164,20 +172,25 @@ def _raw_dict(path, importer=None):
     return workflow
 
 
-def find_tool_ids(path):
-    tool_ids = set()
-    workflow = _raw_dict(path)
-
-    def register_tool_ids(tool_ids, workflow):
-        for step in workflow["steps"].values():
-            if step.get("subworkflow"):
-                register_tool_ids(tool_ids, step["subworkflow"])
-            elif step.get("tool_id"):
-                tool_ids.add(step["tool_id"])
+def get_tool_ids_for_workflow(wf_dict: Dict[str, Any], tool_ids: Optional[List[str]] = None) -> List[str]:
+    tool_ids = [] if tool_ids is None else tool_ids
+    steps = wf_dict["steps"].values() if isinstance(wf_dict["steps"], dict) else wf_dict["steps"]
+    for step in steps:
+        if step.get("type", "tool") == "tool" and not step.get("run", {}).get("class") == "GalaxyWorkflow":
+            tool_id = step["tool_id"]
+            tool_ids.append(tool_id)
+        elif step.get("type") == "subworkflow":  # GA SWF
+            get_tool_ids_for_workflow(step["subworkflow"], tool_ids=tool_ids)
+        elif step.get("run", {}).get("class") == "GalaxyWorkflow":  # gxformat2 SWF
+            get_tool_ids_for_workflow(step["run"], tool_ids=tool_ids)
+        else:
+            continue
+    return list(dict.fromkeys(tool_ids))
 
-    register_tool_ids(tool_ids, workflow)
 
-    return list(tool_ids)
+def find_tool_ids(path):
+    workflow = _raw_dict(path)
+    return get_tool_ids_for_workflow(workflow)
 
 
 WorkflowOutput = namedtuple("WorkflowOutput", ["order_index", "output_name", "label", "optional"])
diff --git a/tests/test_autoupdate.py b/tests/test_autoupdate.py
index 005244ed6..b4a108f90 100644
--- a/tests/test_autoupdate.py
+++ b/tests/test_autoupdate.py
@@ -3,9 +3,9 @@
 
 from galaxy.util import parse_xml_string
 
-from planemo.autoupdate import (
-    get_newest_tool_id,
-    get_shed_tools_conf_string_for_tool_ids,
+from planemo.autoupdate import get_newest_tool_id
+from planemo.galaxy.config import get_shed_tools_conf_string_for_tool_ids
+from planemo.galaxy.workflows import (
     get_tool_ids_for_workflow,
     get_toolshed_url_for_tool_id,
 )