diff --git a/.ci/jenkins/api-py3/run_tests.sh b/.ci/jenkins/api-py3/run_tests.sh
index ff50c56eaf2..24790d0b720 100644
--- a/.ci/jenkins/api-py3/run_tests.sh
+++ b/.ci/jenkins/api-py3/run_tests.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --skip_flakey_fails -api_py3 "$@"
+./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --skip_flakey_fails -api "$@"
diff --git a/.ci/jenkins/framework-py3/run_tests.sh b/.ci/jenkins/framework-py3/run_tests.sh
index 7264876e6df..f8bfe97335d 100644
--- a/.ci/jenkins/framework-py3/run_tests.sh
+++ b/.ci/jenkins/framework-py3/run_tests.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --framework_py3 "$@"
+./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --framework "$@"
diff --git a/.ci/jenkins/integration-py3/run_tests.sh b/.ci/jenkins/integration-py3/run_tests.sh
index 5881c5989a5..b45d68d67b5 100755
--- a/.ci/jenkins/integration-py3/run_tests.sh
+++ b/.ci/jenkins/integration-py3/run_tests.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --integration_py3 "$@"
+./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --integration "$@"
diff --git a/run_tests.sh b/run_tests.sh
index 7ee34fe3317..d922a097057 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -11,7 +11,6 @@ cat <<EOF
 '${0##*/} -sid ccc'                 for testing one section with sid 'ccc' ('ccc' is the string after 'section::')
 '${0##*/} -list'                    for listing all the tool ids
 '${0##*/} -api (test_path)'         for running all the test scripts in the ./test/api directory
-'${0##*/} -api_py3 (test_path)'     for running all the test scripts in the ./test/api directory using python 3
 '${0##*/} -toolshed (test_path)'    for running all the test scripts in the ./test/shed_functional/functional directory
 '${0##*/} -installed'               for running tests of Tool Shed installed tools
 '${0##*/} -framework'               for running through example tool tests testing framework features in test/functional/tools"
@@ -350,21 +349,9 @@ do
           fi
           ;;
       -a|-api|--api)
-          with_framework_test_tools_arg="-with_framework_test_tools"
-          test_script="./scripts/functional_tests.py"
-          report_file="./run_api_tests.html"
-          if [ $# -gt 1 ]; then
-              api_script=$2
-              shift 2
-          else
-              api_script="./test/api"
-              shift 1
-          fi
-          ;;
-      -api_py3|--api_py3)
           with_framework_test_tools_arg="-with_framework_test_tools"
           test_script="pytest"
-          report_file="./run_api_tests_python_3.html"
+          report_file="./run_api_tests.html"
           if [ $# -gt 1 ]; then
               api_script=$2
               shift 2
@@ -429,11 +416,6 @@ do
           framework_test=1;
           shift 1
           ;;
-      -framework_py3|--framework_py3)
-          report_file="run_framework_tests.html"
-          framework_test=1;
-          shift 1
-          ;;
       -d|-data_managers|--data_managers)
           data_managers_test=1;
           shift 1
@@ -503,19 +485,8 @@ do
           fi
           ;;
       -i|-integration|--integration)
-          report_file="run_integration_tests.html"
-          test_script="./scripts/nosetests.py"
-          if [ $# -gt 1 ]; then
-              integration_extra=$2
-              shift 2
-          else
-              integration_extra='test/integration'
-              shift 1
-          fi
-          ;;
-      -integration_py3|--integration_py3)
           test_script="pytest"
-          report_file="./run_api_tests_python_3.html"
+          report_file="./run_integration_tests.html"
           if [ $# -gt 1 ]; then
               integration_extra=$2
               shift 2