diff --git a/run_tests.sh b/run_tests.sh
index 926f2bffd22..ab5184ba069 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -4,9 +4,6 @@ cd "$(dirname "$0")"
 
 show_help() {
 cat <<EOF
-'${0##*/} -id bbb'                  for testing one tool with id 'bbb' ('bbb' is the tool id)
-'${0##*/} -sid ccc'                 for testing one section with sid 'ccc' ('ccc' is the string after 'section::')
-'${0##*/} -list'                    for listing all the tool ids
 '${0##*/} -api (test_path)'         for running all the test scripts in the ./lib/galaxy_test/api directory, test_path
                                     can be pytest selector
 '${0##*/} -cwl (test_path)'         for running all the test scripts in the ./lib/galaxy_test/api/cwl directory, test_path
@@ -14,7 +11,6 @@ cat <<EOF
 '${0##*/} -integration (test_path)' for running all integration test scripts in the ./test/integration directory, test_path
                                     can be pytest selector
 '${0##*/} -toolshed (test_path)'    for running all the test scripts in the ./lib/tool_shed/test directory
-'${0##*/} -installed'               for running tests of Tool Shed installed tools
 '${0##*/} -main'                    for running tests of tools shipped with Galaxy
 '${0##*/} -framework'               for running through example tool tests testing framework features in test/functional/tools"
 '${0##*/} -framework -id toolid'    for testing one framework tool (in test/functional/tools/) with id 'toolid'
@@ -297,7 +293,6 @@ if [ -n "$BUILD_NUMBER" ]; then
     xunit_report_file="xunit-${BUILD_NUMBER}.xml"
 fi
 
-run_default_functional_tests="1"
 # Loop through and consume the main arguments.
 # Some loops will consume more than one argument (there are extra "shift"s in some cases).
 while :
@@ -307,10 +302,6 @@ do
           show_help
           exit 0
           ;;
-      -l|-list|--list)
-          show_list
-          exit 0
-          ;;
       -id|--id)
           if [ $# -gt 1 ]; then
               test_id=$2;
@@ -320,15 +311,6 @@ do
               exit 1
           fi
           ;;
-      -s|-sid|--sid)
-          if [ $# -gt 1 ]; then
-              section_id=$2
-              shift 2
-          else
-              echo "--sid requires an argument" 1>&2
-              exit 1
-          fi
-          ;;
       -a|-api|--api)
           GALAXY_TEST_USE_HIERARCHICAL_OBJECT_STORE="True"  # Run these tests with a non-trivial object store.
           export GALAXY_TEST_USE_HIERARCHICAL_OBJECT_STORE
@@ -409,32 +391,18 @@ do
           framework_test=1;
           shift 1
           ;;
-      -main|-main_tools|--main_tools)
-          GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample"
-          marker="tool"
-          report_file="run_framework_tests.html"
-          framework_test=1;
-          shift 1
-          ;;
       -d|-data_managers|--data_managers)
           marker="data_manager"
           report_file="run_data_managers_tests.html"
           data_managers_test=1;
           shift 1
           ;;
-      -m|-migrated|--migrated)
-          GALAXY_TEST_TOOL_CONF="config/migrated_tools_conf.xml"
+      -main|-main_tools|--main_tools)
+          GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample"
           marker="tool"
-          report_file="run_migrated_tests.html"
-          migrated_test=1;
-          shift
-          ;;
-      -installed|--installed)
-          GALAXY_TEST_TOOL_CONF="config/shed_tool_conf.xml"
-          marker="tool"
-          report_file="run_installed_tests.html"
-          installed_test=1;
-          shift
+          report_file="run_framework_tests.html"
+          framework_test=1;
+          shift 1
           ;;
       -r|--report_file)
           if [ $# -gt 1 ]; then
@@ -555,7 +523,6 @@ do
       --)
           # Do not default to running the functional tests in this case, caller
           # is opting to run specific tests so don't interfere with that by default.
-          unset run_default_functional_tests;
           shift
           break
           ;;
@@ -589,7 +556,7 @@ fi
 
 setup_python
 
-if [ -n "$framework_test" ] || [ -n "$installed_test" ] || [ -n "$migrated_test" ] || [ -n "$data_managers_test" ] ; then
+if [ -n "$framework_test" ] || [ -n "$data_managers_test" ] ; then
     if [ -n "$test_id" ]; then
         selector="-k $test_id"
     else
@@ -602,16 +569,12 @@ elif [ -n "$toolshed_script" ]; then
     extra_args="$toolshed_script"
 elif [ -n "$api_script" ]; then
     extra_args="$api_script"
-elif [ -n "$section_id" ]; then
-    extra_args=$(python tool_list.py "$section_id")
 elif [ -n "$unit_extra" ]; then
     extra_args="$unit_extra"
 elif [ -n "$integration_extra" ]; then
     extra_args="$integration_extra"
 elif [ -n "$test_target" ] ; then
     extra_args="$test_target"
-elif [ -n "$run_default_functional_tests" ] ; then
-    extra_args='--exclude="^get" functional'
 else
     extra_args=""
 fi
diff --git a/tool_list.py b/tool_list.py
deleted file mode 100644
index d335805d1fc..00000000000
--- a/tool_list.py
+++ /dev/null
@@ -1,85 +0,0 @@
-import os
-import sys
-
-# read tool_conf.xml to get all the tool xml file names
-onoff = 1
-tool_list = []
-tool_conf_file = os.environ.get("GALAXY_TEST_TOOL_CONF", None)
-
-if tool_conf_file is None:
-    for possible_tool_file in ["config/tool_conf.xml", "tool_conf.xml", "config/tool_conf.xml.sample"]:
-        tool_conf_file = possible_tool_file
-        if os.path.isfile(possible_tool_file):
-            break
-
-if tool_conf_file is None or not os.path.isfile(tool_conf_file):
-    sys.stderr.write(f"Tool config file not found: {tool_conf_file}\n")
-    sys.exit(1)
-
-for line in open(tool_conf_file):
-    if line.find("<!--") != -1:
-        onoff = 0
-    if line.find("file") != -1 and onoff == 1:
-        strs = line.split('"')
-        tool_list.append(strs[1])
-    if line.find("<section") != -1 and onoff == 1:
-        keys = line.strip().split('"')
-        n = 0
-        strtmp = "section::"
-        while n < len(keys):
-            if keys[n].find("id") != -1:
-                strtmp = strtmp + keys[n + 1]
-            if keys[n].find("name") != -1:
-                strtmp = strtmp + keys[n + 1] + "-"
-            n = n + 1
-        tool_list.append(strtmp.replace(" ", "_"))
-    if line.find("-->") != -1:
-        onoff = 1
-
-# read tool info from every tool xml file
-name = []
-id = []
-desc = []
-tool_infos = []
-for tool in tool_list:
-    if tool.find("section") != -1:
-        tool_info = dict()
-        tool_info["id"] = tool
-        tool_infos.append(tool_info)
-    if os.path.exists("tools/" + tool):
-        for line in open("tools/" + tool):
-            if line.find("<tool ") != -1 and line.find("id") != -1:
-                keys = line.strip().split('"')
-                tool_info = dict()
-                tool_info["desc"] = ""
-                for n in range(len(keys) - 1):
-                    if " id=" in keys[n]:
-                        tool_info["id"] = keys[n + 1].replace(" ", "_")
-                    if " name=" in keys[n]:
-                        tool_info["name"] = keys[n + 1]
-                    if " description=" in keys[n]:
-                        tool_info["desc"] = keys[n + 1]
-                tool_infos.append(tool_info)
-                break
-
-flag = 0
-if len(sys.argv) == 1:
-    for tool_info in tool_infos:
-        if tool_info["id"].find("section") != -1:
-            print(
-                "==========================================================================================================================================="
-            )
-            print("{:<45}\t{:<40}\t{}".format("id", "name", tool_info["id"]))
-            print(
-                "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -"
-            )
-        else:
-            print("{:<45}\t{:<40}".format(tool_info["id"], tool_info["name"]))
-else:
-    for tool_info in tool_infos:
-        if tool_info["id"].find("section") != -1:
-            flag = 0
-        elif flag == 1:
-            print(" functional.test_toolbox:TestForTool_%s" % tool_info["id"], end=" ")
-        if tool_info["id"].replace("section::", "") == sys.argv[1]:
-            flag = 1