diff --git a/run_tests.sh b/run_tests.sh
index 35e46a1b4374..bd5df9e32336 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -2,8 +2,6 @@
 
 cd "$(dirname "$0")"
 
-rm -f run_functional_tests.log
-
 show_help() {
 cat <<EOF
 '${0##*/} -id bbb'                  for testing one tool with id 'bbb' ('bbb' is the tool id)
@@ -27,7 +25,7 @@ cat <<EOF
 '${0##*/} -selenium (test_selector)' for running specified selenium web tests (using pytest selector syntax)
 
 This wrapper script largely serves as a point documentation and convenience for
-running Galaxy's Python tests. Most Python tests shipped with Galaxy can be run with
+running Galaxy's Python tests. All Python tests shipped with Galaxy can be run with
 pytest directly. Galaxy's client unit tests can be run with ``make client-test``
 or ``yarn`` directly as documented in detail in ``client/README.md``.
 
@@ -52,7 +50,7 @@ The main test types are as follows:
    framework twill to test ToolShed related functionality. These are
    located in lib/tool_shed/test.
 
-Python testing is mostly done via pytest. Specific tests can be selected
+Python testing is done via pytest. Specific tests can be selected
 using the pytest selector syntax is described at https://docs.pytest.org/en/latest/usage.html.
 
 The spots these selectors can be used is described in the above usage documentation
@@ -152,7 +150,7 @@ Extra options:
  --no_cleanup          Do not delete temp files for Python functional tests
                        (-toolshed, -framework, etc...)
  --coverage            Generate a test coverage report. This option currently
-                       should work with every test that uses pytest, but the
+                       works with every python test, but the
                        results may not be reliable with selenium or other
                        frameworks that primarily test the client.
  --debug               On python test error or failure invoke a pdb shell for
@@ -270,7 +268,7 @@ exists() {
 }
 
 debug=""
-test_script="./scripts/functional_tests.py"
+test_script="pytest"
 report_file="run_functional_tests.html"
 coverage_arg=""
 xunit_report_file=""
@@ -327,7 +325,6 @@ do
           export GALAXY_TEST_USE_HIERARCHICAL_OBJECT_STORE
           GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
           marker="not cwl_conformance"
-          test_script="pytest"
           report_file="./run_api_tests.html"
           if [ $# -gt 1 ]; then
               api_script=$2
@@ -342,7 +339,6 @@ do
           export GALAXY_TEST_USE_HIERARCHICAL_OBJECT_STORE
           GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
           marker="cwl_conformance"
-          test_script="pytest"
           report_file="./run_cwl_tests.html"
           generate_cwl_conformance_tests=1
           if [ $# -gt 1 ]; then
@@ -355,7 +351,6 @@ do
           ;;
       -selenium|--selenium)
           GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
-          test_script="pytest"
           report_file="./run_selenium_tests.html"
           skip_client_build=""
           if [ $# -gt 1 ]; then
@@ -367,7 +362,6 @@ do
           fi
           ;;
       -t|-toolshed|--toolshed)
-          test_script="./lib/tool_shed/test/functional_tests.py"
           report_file="run_toolshed_tests.html"
           if [ $# -gt 1 ]; then
               toolshed_script=$2
@@ -402,7 +396,6 @@ do
       -f|-framework|--framework)
           GALAXY_TEST_TOOL_CONF="test/functional/tools/samples_tool_conf.xml"
           marker="tool"
-          test_script="pytest"
           report_file="run_framework_tests.html"
           framework_test=1;
           shift 1
@@ -410,14 +403,12 @@ do
       -main|-main_tools|--main_tools)
           GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample"
           marker="tool"
-          test_script="pytest"
           report_file="run_framework_tests.html"
           framework_test=1;
           shift 1
           ;;
       -d|-data_managers|--data_managers)
           marker="data_manager"
-          test_script="pytest"
           report_file="run_data_managers_tests.html"
           data_managers_test=1;
           shift 1
@@ -425,7 +416,6 @@ do
       -m|-migrated|--migrated)
           GALAXY_TEST_TOOL_CONF="config/migrated_tools_conf.xml"
           marker="tool"
-          test_script="pytest"
           report_file="run_migrated_tests.html"
           migrated_test=1;
           shift
@@ -433,7 +423,6 @@ do
       -installed|--installed)
           GALAXY_TEST_TOOL_CONF="config/shed_tool_conf.xml"
           marker="tool"
-          test_script="pytest"
           report_file="run_installed_tests.html"
           installed_test=1;
           shift
@@ -501,7 +490,6 @@ do
           ;;
       -u|-unit|--unit)
           report_file="run_unit_tests.html"
-          test_script="pytest"
           unit_extra='--doctest-modules --ignore lib/galaxy/web/proxy/js/node_modules/ --ignore lib/tool_shed/webapp/controllers --ignore lib/galaxy/jobs/runners/chronos.py --ignore lib/tool_shed/webapp/model/migrate --ignore lib/galaxy/tools/bundled --ignore lib/galaxy_test --ignore lib/tool_shed/test --ignore lib/galaxy/model/migrations/alembic'
           generate_cwl_conformance_tests=1
           if [ $# -gt 1 ]; then
@@ -514,7 +502,6 @@ do
           ;;
       -i|-integration|--integration)
           GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
-          test_script="pytest"
           report_file="./run_integration_tests.html"
           if [ $# -gt 1 ]; then
               integration_extra=$2
@@ -621,20 +608,12 @@ else
 fi
 
 if [ -n "$xunit_report_file" ]; then
-    if [ "$test_script" = 'pytest' ]; then
-        xunit_args="--junit-xml $xunit_report_file"
-    else
-        xunit_args="--with-xunit --xunit-file $xunit_report_file"
-    fi
+    xunit_args="--junit-xml $xunit_report_file"
 else
     xunit_args=""
 fi
 if [ -n "$structured_data_report_file" ]; then
-    if [ "$test_script" = 'pytest' ]; then
-        structured_data_args="--json-report --json-report-file $structured_data_report_file"
-    else
-        structured_data_args="--with-structureddata --structured-data-file $structured_data_report_file"
-    fi
+    structured_data_args="--json-report --json-report-file $structured_data_report_file"
 else
     structured_data_args=""
 fi
@@ -642,20 +621,16 @@ if [ -n "$generate_cwl_conformance_tests" ]; then
     make generate-cwl-conformance-tests
 fi
 export GALAXY_TEST_TOOL_CONF
-if [ "$test_script" = 'pytest' ]; then
-    if [ "$coverage_arg" = '--with-coverage' ]; then
-        coverage_arg="--cov-report xml --cov-report term --cov=lib"
-    fi
-    if [ -n "$marker" ]; then
-        marker_args=(-m "$marker")
-    else
-        marker_args=()
-    fi
-    args=(-v $debug $structured_data_args --html "$report_file" --self-contained-html $coverage_arg $xunit_args $extra_args "${marker_args[@]}" "$@")
-    "$test_script" "${args[@]}"
+if [ "$coverage_arg" = '--with-coverage' ]; then
+    coverage_arg="--cov-report xml --cov-report term --cov=lib"
+fi
+if [ -n "$marker" ]; then
+    marker_args=(-m "$marker")
 else
-    python "$test_script" $coverage_arg -v --html-report-file $report_file $xunit_args $structured_data_args $extra_args "$@"
+    marker_args=()
 fi
+args=(-v $debug $structured_data_args --html "$report_file" --self-contained-html $coverage_arg $xunit_args $extra_args "${marker_args[@]}" "$@")
+"$test_script" "${args[@]}"
 exit_status=$?
 echo "Testing complete. HTML report is in \"$report_file\"." 1>&2
 if [ "$structured_data_html" = '1' ]; then
diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py
deleted file mode 100644
index 06b07506674a..000000000000
--- a/scripts/functional_tests.py
+++ /dev/null
@@ -1,132 +0,0 @@
-#!/usr/bin/env python
-"""Test driver for many Galaxy Python functional tests.
-
-Launch this script by running ``run_tests.sh`` from GALAXY_ROOT, see
-that script for a list of options.
-"""
-
-import os
-import os.path
-import sys
-
-galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir))
-sys.path[1:1] = [os.path.join(galaxy_root, "lib"), os.path.join(galaxy_root, "test")]
-
-from galaxy.util import classproperty
-from galaxy_test.base.api_util import (
-    get_admin_api_key,
-    get_user_api_key,
-)
-from galaxy_test.driver import driver_util
-
-log = driver_util.build_logger()
-
-
-class MigratedToolsGalaxyTestDriver(driver_util.GalaxyTestDriver):
-    """Instantiate a Galaxy-style TestDriver for testing migrated Galaxy tools."""
-
-    testing_shed_tools = True
-
-    def build_tests(self):
-        """Build migrated tool test methods."""
-        self.setup_shed_tools(
-            testing_migrated_tools=True,
-        )
-        self.build_tool_tests()
-
-
-class InstalledToolsGalaxyTestDriver(driver_util.GalaxyTestDriver):
-    """Galaxy-style TestDriver for testing installed Galaxy tools."""
-
-    testing_shed_tools = True
-
-    def build_tests(self):
-        """Build installed tool test methods."""
-        self.setup_shed_tools(
-            testing_installed_tools=True,
-        )
-        self.build_tool_tests()
-
-
-class DefaultGalaxyTestDriver(driver_util.GalaxyTestDriver):
-    """Default Galaxy-style nose test driver.
-
-    Just populate non-shed tool tests and run tests. Works
-    for tool tests, regular twill tests, and API testing.
-    """
-
-    def build_tests(self):
-        """Build framework tool test methods."""
-        self.build_tool_tests()
-
-
-class SeleniumGalaxyTestDriver(driver_util.GalaxyTestDriver):
-    """Galaxy-style TestDriver for selenium framework testing."""
-
-    framework_tool_and_types = True
-
-    @classproperty
-    def default_web_host(cls):
-        from galaxy_test.selenium.framework import default_web_host_for_selenium_tests
-
-        return default_web_host_for_selenium_tests()
-
-
-class FrameworkToolsGalaxyTestDriver(DefaultGalaxyTestDriver):
-    """Galaxy-style TestDriver for testing framework Galaxy tools."""
-
-    framework_tool_and_types = True
-    conda_auto_init = True
-    conda_auto_install = True
-
-
-class DataManagersGalaxyTestDriver(driver_util.GalaxyTestDriver):
-    """Galaxy-style TestDriver for testing framework Galaxy tools."""
-
-    def build_tests(self):
-        """Build data manager test methods."""
-        import functional.test_data_managers
-
-        functional.test_data_managers.data_managers = self.app.data_managers
-        functional.test_data_managers.build_tests(
-            tmp_dir=self.galaxy_test_tmp_dir,
-            testing_shed_tools=self.testing_shed_tools,
-            master_api_key=get_admin_api_key(),
-            user_api_key=get_user_api_key(),
-            user_email=self.app.config.admin_users_list[0],
-            create_admin=True,
-        )
-
-
-TEST_DRIVERS = {
-    "-migrated": MigratedToolsGalaxyTestDriver,
-    "-installed": InstalledToolsGalaxyTestDriver,
-    "-framework": FrameworkToolsGalaxyTestDriver,
-    "-data_managers": DataManagersGalaxyTestDriver,
-    "-selenium": SeleniumGalaxyTestDriver,
-}
-
-
-def find_test_driver():
-    """Look at command-line args and find the correct Galaxy test driver."""
-    test_driver = DefaultGalaxyTestDriver
-
-    for key in TEST_DRIVERS.keys():
-        if _check_arg(key):
-            test_driver = TEST_DRIVERS[key]
-
-    return test_driver
-
-
-def _check_arg(name):
-    try:
-        index = sys.argv.index(name)
-        del sys.argv[index]
-        ret_val = True
-    except ValueError:
-        ret_val = False
-    return ret_val
-
-
-if __name__ == "__main__":
-    driver_util.drive_test(find_test_driver())