diff --git a/src/ephemeris/shed_tools.py b/src/ephemeris/shed_tools.py
index 76f0019..59f2a1e 100644
--- a/src/ephemeris/shed_tools.py
+++ b/src/ephemeris/shed_tools.py
@@ -689,15 +689,19 @@ def main(argv=None):
     else:
         tool_list = dict()
 
-    # Get some of the other installation arguments
-    kwargs = dict(
-        default_install_tool_dependencies=tool_list.get("install_tool_dependencies")
-        or getattr(args, "install_tool_dependencies", False),
-        default_install_repository_dependencies=tool_list.get("install_repository_dependencies")
-        or getattr(args, "install_repository_dependencies", False),
-        default_install_resolver_dependencies=tool_list.get("install_resolver_dependencies")
-        or getattr(args, "install_resolver_dependencies", False),
-    )
+    # Command line arguments should take precedence over arguments in the tool list,
+    # but only if the command line argument has actually been used.
+    kwargs = {}
+    for arg in ['install_tool_dependencies', 'install_repository_dependencies', 'install_resolver_dependencies']:
+        if not getattr(args, f"{arg}_set", False):
+            # commandline argument not set, use tool_list argument
+            arg_val = tool_list.get(arg)
+            if arg_val is None:
+                # Not specified in yaml file, use command line default, even if not set
+                arg_val = getattr(args, arg, False)
+        else:
+            arg_val = getattr(args, arg)
+        kwargs[f"default_{arg}"] = arg_val
 
     # Start installing/updating and store the results in install_results.
     # Or do testing if the action is `test`
diff --git a/src/ephemeris/shed_tools_args.py b/src/ephemeris/shed_tools_args.py
index 18ec43c..9ecfc2a 100644
--- a/src/ephemeris/shed_tools_args.py
+++ b/src/ephemeris/shed_tools_args.py
@@ -8,6 +8,23 @@
 )
 
 
+class StoredTrue(argparse.Action):
+
+    _value = True
+
+    def __init__(self, option_strings, dest, nargs=0, **kwargs):
+        super().__init__(option_strings, dest, nargs=nargs, **kwargs)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        setattr(namespace, self.dest + '_set', True)
+        setattr(namespace, self.dest, self._value)
+
+
+class StoredFalse(StoredTrue):
+
+    _value = False
+
+
 def parser():
     """construct the parser object"""
     common_arguments = get_common_args(log_file=True)
@@ -120,7 +137,7 @@ def parser():
         command_parser.add_argument(
             "--skip-install-tool-dependencies",
             "--skip_install_tool_dependencies",
-            action="store_false",
+            action=StoredFalse,
             dest="install_tool_dependencies",
             default=False,  # Override True default for this function
             help=argparse.SUPPRESS,
@@ -128,7 +145,7 @@ def parser():
         command_parser.add_argument(
             "--install-tool-dependencies",
             "--install_tool_dependencies",
-            action="store_true",
+            action=StoredTrue,
             dest="install_tool_dependencies",
             help="Turn on installation of tool dependencies using classic toolshed packages. "
             "Can be overwritten on a per-tool basis in the tools file.",
@@ -136,7 +153,7 @@ def parser():
         command_parser.add_argument(
             "--install-resolver-dependencies",
             "--install_resolver_dependencies",
-            action="store_true",
+            action=StoredTrue,
             dest="install_resolver_dependencies",
             default=True,  # Override False default for this function
             help=argparse.SUPPRESS,
@@ -144,7 +161,7 @@ def parser():
         command_parser.add_argument(
             "--skip-install-resolver-dependencies",
             "--skip_install_resolver_dependencies",
-            action="store_false",
+            action=StoredFalse,
             dest="install_resolver_dependencies",
             help="Skip installing tool dependencies through resolver (e.g. conda). "
             "Will be ignored on galaxy releases older than 16.07. "
@@ -153,7 +170,7 @@ def parser():
         command_parser.add_argument(
             "--skip-install-repository-dependencies",
             "--skip_install_repository_dependencies",
-            action="store_false",
+            action=StoredFalse,
             dest="install_repository_dependencies",
             help="Skip installing the repository dependencies.",
         )
diff --git a/tests/test_run_data_managers.py b/tests/test_run_data_managers.py
index d12f527..5174a9b 100644
--- a/tests/test_run_data_managers.py
+++ b/tests/test_run_data_managers.py
@@ -21,9 +21,15 @@ def test_install_data_managers(self, start_container):
         """Install the data_managers on galaxy"""
         container = start_container
         data_managers = [
-            dict(name="data_manager_fetch_genome_dbkeys_all_fasta", owner="devteam"),
-            dict(name="data_manager_sam_fasta_index_builder", owner="devteam"),
-            dict(name="data_manager_bwa_mem_index_builder", owner="devteam"),
+            dict(name="data_manager_fetch_genome_dbkeys_all_fasta",
+                 owner="devteam",
+                 install_resolver_dependencies=True),
+            dict(name="data_manager_sam_fasta_index_builder",
+                 owner="devteam",
+                 install_resolver_dependencies=True),
+            dict(name="data_manager_bwa_mem_index_builder",
+                 owner="devteam",
+                 install_resolver_dependencies=True)
         ]
         irm = InstallRepositoryManager(container.gi)
         irm.install_repositories(data_managers)