diff --git a/run_tests.sh b/run_tests.sh
index e5c13aa9e20..ff9cd96b7d5 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -13,7 +13,7 @@ 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##*/} -toolshed (test_path)'    for running all the test scripts in the ./test/tool_shed/functional directory
+'${0##*/} -toolshed (test_path)'    for running all the test scripts in the ./test/shed_functional/functional directory
 '${0##*/} -workflow test.xml'       for running a workflow test case as defined by supplied workflow xml test file (experimental)
 '${0##*/} -installed'               for running tests of Tool Shed installed tools
 '${0##*/} -framework'               for running through example tool tests testing framework features in test/functional/tools"
@@ -135,7 +135,7 @@ GALAXY_TEST_SHED_TOOL_CONF      Shed toolbox conf (defaults to
                                 installed to tools with -installed.
 TOOL_SHED_TEST_HOST             Host to use for shed server setup for testing.
 TOOL_SHED_TEST_PORT             Port to use for shed server setup for testing.
-TOOL_SHED_TEST_FILE_DIR         Defaults to test/tool_shed/test_data.
+TOOL_SHED_TEST_FILE_DIR         Defaults to test/shed_functional/test_data.
 TOOL_SHED_TEST_TMP_DIR          Defaults to random /tmp directory - place for
                                 tool shed test server files to be placed.
 TOOL_SHED_TEST_OMIT_GALAXY      Do not launch a Galaxy server for tool shed
@@ -247,13 +247,13 @@ do
           fi
           ;;
       -t|-toolshed|--toolshed)
-          test_script="./test/tool_shed/functional_tests.py"
+          test_script="./test/shed_functional/functional_tests.py"
           report_file="run_toolshed_tests.html"
           if [ $# -gt 1 ]; then
               toolshed_script=$2
               shift 2
           else
-              toolshed_script="./test/tool_shed/functional"
+              toolshed_script="./test/shed_functional/functional"
               shift 1
           fi
           ;;
diff --git a/test/base/driver_util.py b/test/base/driver_util.py
index 2cbb026f6cb..e980ac20d2d 100644
--- a/test/base/driver_util.py
+++ b/test/base/driver_util.py
@@ -41,7 +41,7 @@ galaxy_root = os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pa
 DEFAULT_WEB_HOST = "localhost"
 GALAXY_TEST_DIRECTORY = os.path.join(galaxy_root, "test")
 GALAXY_TEST_FILE_DIR = "test-data,https://github.com/galaxyproject/galaxy-test-data.git"
-TOOL_SHED_TEST_DATA = os.path.join(GALAXY_TEST_DIRECTORY, "tool_shed", "test_data")
+TOOL_SHED_TEST_DATA = os.path.join(GALAXY_TEST_DIRECTORY, "shed_functional", "test_data")
 FRAMEWORK_TOOLS_DIR = os.path.join(GALAXY_TEST_DIRECTORY, "functional", "tools")
 FRAMEWORK_UPLOAD_TOOL_CONF = os.path.join(FRAMEWORK_TOOLS_DIR, "upload_tool_conf.xml")
 FRAMEWORK_SAMPLE_TOOLS_CONF = os.path.join(FRAMEWORK_TOOLS_DIR, "samples_tool_conf.xml")
diff --git a/test/tool_shed/__init__.py b/test/shed_functional/__init__.py
similarity index 100%
rename from test/tool_shed/__init__.py
rename to test/shed_functional/__init__.py
diff --git a/test/tool_shed/base/__init__.py b/test/shed_functional/base/__init__.py
similarity index 100%
rename from test/tool_shed/base/__init__.py
rename to test/shed_functional/base/__init__.py
diff --git a/test/tool_shed/base/common.py b/test/shed_functional/base/common.py
similarity index 100%
rename from test/tool_shed/base/common.py
rename to test/shed_functional/base/common.py
diff --git a/test/tool_shed/base/test_db_util.py b/test/shed_functional/base/test_db_util.py
similarity index 100%
rename from test/tool_shed/base/test_db_util.py
rename to test/shed_functional/base/test_db_util.py
diff --git a/test/tool_shed/base/twilltestcase.py b/test/shed_functional/base/twilltestcase.py
similarity index 100%
rename from test/tool_shed/base/twilltestcase.py
rename to test/shed_functional/base/twilltestcase.py
diff --git a/test/tool_shed/functional/__init__.py b/test/shed_functional/functional/__init__.py
similarity index 100%
rename from test/tool_shed/functional/__init__.py
rename to test/shed_functional/functional/__init__.py
diff --git a/test/tool_shed/functional/test_0000_basic_repository_features.py b/test/shed_functional/functional/test_0000_basic_repository_features.py
similarity index 99%
rename from test/tool_shed/functional/test_0000_basic_repository_features.py
rename to test/shed_functional/functional/test_0000_basic_repository_features.py
index 18fdb8f1590..f8b1b98f960 100644
--- a/test/tool_shed/functional/test_0000_basic_repository_features.py
+++ b/test/shed_functional/functional/test_0000_basic_repository_features.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 repository_name = 'filtering_0000'
 repository_description = "Galaxy's filtering tool for test 0000"
diff --git a/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py b/test/shed_functional/functional/test_0010_repository_with_tool_dependencies.py
similarity index 99%
rename from test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py
rename to test/shed_functional/functional/test_0010_repository_with_tool_dependencies.py
index b5643c6c0cf..f11f262c286 100644
--- a/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py
+++ b/test/shed_functional/functional/test_0010_repository_with_tool_dependencies.py
@@ -1,6 +1,6 @@
 import os
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 repository_name = 'freebayes_0010'
 repository_description = "Galaxy's freebayes tool"
diff --git a/test/tool_shed/functional/test_0020_basic_repository_dependencies.py b/test/shed_functional/functional/test_0020_basic_repository_dependencies.py
similarity index 98%
rename from test/tool_shed/functional/test_0020_basic_repository_dependencies.py
rename to test/shed_functional/functional/test_0020_basic_repository_dependencies.py
index 6b415bd7516..b76f0960fea 100644
--- a/test/tool_shed/functional/test_0020_basic_repository_dependencies.py
+++ b/test/shed_functional/functional/test_0020_basic_repository_dependencies.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 datatypes_repository_name = 'emboss_datatypes_0020'
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
diff --git a/test/tool_shed/functional/test_0030_repository_dependency_revisions.py b/test/shed_functional/functional/test_0030_repository_dependency_revisions.py
similarity index 99%
rename from test/tool_shed/functional/test_0030_repository_dependency_revisions.py
rename to test/shed_functional/functional/test_0030_repository_dependency_revisions.py
index 4cf447b733e..7aa00ac343c 100644
--- a/test/tool_shed/functional/test_0030_repository_dependency_revisions.py
+++ b/test/shed_functional/functional/test_0030_repository_dependency_revisions.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 datatypes_repository_name = 'emboss_datatypes_0030'
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
diff --git a/test/tool_shed/functional/test_0040_repository_circular_dependencies.py b/test/shed_functional/functional/test_0040_repository_circular_dependencies.py
similarity index 99%
rename from test/tool_shed/functional/test_0040_repository_circular_dependencies.py
rename to test/shed_functional/functional/test_0040_repository_circular_dependencies.py
index fc0b518d823..6d01c3c3964 100644
--- a/test/tool_shed/functional/test_0040_repository_circular_dependencies.py
+++ b/test/shed_functional/functional/test_0040_repository_circular_dependencies.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 freebayes_repository_name = 'freebayes_0040'
 freebayes_repository_description = "Galaxy's freebayes tool for test 0040"
diff --git a/test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py b/test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py
similarity index 99%
rename from test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py
rename to test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py
index 029184e2fde..67cef36ea29 100644
--- a/test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py
+++ b/test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 emboss_datatypes_repository_name = 'emboss_datatypes_0050'
 emboss_datatypes_repository_description = "Datatypes for emboss"
diff --git a/test/tool_shed/functional/test_0060_workflows.py b/test/shed_functional/functional/test_0060_workflows.py
similarity index 99%
rename from test/tool_shed/functional/test_0060_workflows.py
rename to test/shed_functional/functional/test_0060_workflows.py
index a62fd6b9c73..f9e86fe782a 100644
--- a/test/tool_shed/functional/test_0060_workflows.py
+++ b/test/shed_functional/functional/test_0060_workflows.py
@@ -1,6 +1,6 @@
 import os
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 repository_name = 'filtering_0060'
 repository_description = "Galaxy's filtering tool for test 0060"
diff --git a/test/tool_shed/functional/test_0070_invalid_tool.py b/test/shed_functional/functional/test_0070_invalid_tool.py
similarity index 98%
rename from test/tool_shed/functional/test_0070_invalid_tool.py
rename to test/shed_functional/functional/test_0070_invalid_tool.py
index 0c7e3c26867..800281281f4 100644
--- a/test/tool_shed/functional/test_0070_invalid_tool.py
+++ b/test/shed_functional/functional/test_0070_invalid_tool.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 repository_name = 'bismark_0070'
 repository_description = "Galaxy's bismark wrapper"
diff --git a/test/tool_shed/functional/test_0080_advanced_circular_dependencies.py b/test/shed_functional/functional/test_0080_advanced_circular_dependencies.py
similarity index 98%
rename from test/tool_shed/functional/test_0080_advanced_circular_dependencies.py
rename to test/shed_functional/functional/test_0080_advanced_circular_dependencies.py
index 18d599d9d57..757935c00d2 100644
--- a/test/tool_shed/functional/test_0080_advanced_circular_dependencies.py
+++ b/test/shed_functional/functional/test_0080_advanced_circular_dependencies.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 column_repository_name = 'column_maker_0080'
 column_repository_description = "Add column"
diff --git a/test/tool_shed/functional/test_0090_tool_search.py b/test/shed_functional/functional/test_0090_tool_search.py
similarity index 99%
rename from test/tool_shed/functional/test_0090_tool_search.py
rename to test/shed_functional/functional/test_0090_tool_search.py
index 1e1530c48b3..6388c2ff573 100644
--- a/test/tool_shed/functional/test_0090_tool_search.py
+++ b/test/shed_functional/functional/test_0090_tool_search.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 emboss_datatypes_repository_name = 'emboss_datatypes_0090'
 emboss_datatypes_repository_description = "Datatypes for emboss"
diff --git a/test/tool_shed/functional/test_0100_complex_repository_dependencies.py b/test/shed_functional/functional/test_0100_complex_repository_dependencies.py
similarity index 99%
rename from test/tool_shed/functional/test_0100_complex_repository_dependencies.py
rename to test/shed_functional/functional/test_0100_complex_repository_dependencies.py
index ebcea165229..71e003e0240 100644
--- a/test/tool_shed/functional/test_0100_complex_repository_dependencies.py
+++ b/test/shed_functional/functional/test_0100_complex_repository_dependencies.py
@@ -1,7 +1,7 @@
 import logging
 import os
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py b/test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py
similarity index 99%
rename from test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py
rename to test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py
index 5dce843f86a..da4ee4a3f69 100644
--- a/test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py
+++ b/test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 datatypes_repository_name = 'emboss_datatypes_0110'
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
diff --git a/test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py b/test/shed_functional/functional/test_0120_simple_repository_dependency_multiple_owners.py
similarity index 99%
rename from test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py
rename to test/shed_functional/functional/test_0120_simple_repository_dependency_multiple_owners.py
index 25736df9833..1e40daf8512 100644
--- a/test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py
+++ b/test/shed_functional/functional/test_0120_simple_repository_dependency_multiple_owners.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 datatypes_repository_name = 'blast_datatypes_0120'
 datatypes_repository_description = 'Galaxy applicable datatypes for BLAST'
diff --git a/test/tool_shed/functional/test_0130_datatype_converters.py b/test/shed_functional/functional/test_0130_datatype_converters.py
similarity index 98%
rename from test/tool_shed/functional/test_0130_datatype_converters.py
rename to test/shed_functional/functional/test_0130_datatype_converters.py
index 20cc822ba78..8bbbb848192 100644
--- a/test/tool_shed/functional/test_0130_datatype_converters.py
+++ b/test/shed_functional/functional/test_0130_datatype_converters.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 repository_name = 'bed_to_gff_0130'
 repository_description = "Converter: BED to GFF"
diff --git a/test/tool_shed/functional/test_0140_tool_help_images.py b/test/shed_functional/functional/test_0140_tool_help_images.py
similarity index 98%
rename from test/tool_shed/functional/test_0140_tool_help_images.py
rename to test/shed_functional/functional/test_0140_tool_help_images.py
index 0398fd186ed..36786d627a9 100644
--- a/test/tool_shed/functional/test_0140_tool_help_images.py
+++ b/test/shed_functional/functional/test_0140_tool_help_images.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger(__name__)
 
diff --git a/test/tool_shed/functional/test_0150_prior_installation_required.py b/test/shed_functional/functional/test_0150_prior_installation_required.py
similarity index 98%
rename from test/tool_shed/functional/test_0150_prior_installation_required.py
rename to test/shed_functional/functional/test_0150_prior_installation_required.py
index 8a3b9bb1950..ffd0cdda0a0 100644
--- a/test/tool_shed/functional/test_0150_prior_installation_required.py
+++ b/test/shed_functional/functional/test_0150_prior_installation_required.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 column_repository_name = 'column_maker_0150'
 column_repository_description = "Add column"
diff --git a/test/tool_shed/functional/test_0160_circular_prior_installation_required.py b/test/shed_functional/functional/test_0160_circular_prior_installation_required.py
similarity index 99%
rename from test/tool_shed/functional/test_0160_circular_prior_installation_required.py
rename to test/shed_functional/functional/test_0160_circular_prior_installation_required.py
index c72bd06bc41..c3fa3f44b81 100644
--- a/test/tool_shed/functional/test_0160_circular_prior_installation_required.py
+++ b/test/shed_functional/functional/test_0160_circular_prior_installation_required.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 filter_repository_name = 'filtering_0160'
 filter_repository_description = "Galaxy's filtering tool for test 0160"
diff --git a/test/tool_shed/functional/test_0170_complex_prior_installation_required.py b/test/shed_functional/functional/test_0170_complex_prior_installation_required.py
similarity index 99%
rename from test/tool_shed/functional/test_0170_complex_prior_installation_required.py
rename to test/shed_functional/functional/test_0170_complex_prior_installation_required.py
index e7055e64c68..5b203f0c539 100644
--- a/test/tool_shed/functional/test_0170_complex_prior_installation_required.py
+++ b/test/shed_functional/functional/test_0170_complex_prior_installation_required.py
@@ -1,6 +1,6 @@
 import os
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 matplotlib_repository_name = 'package_matplotlib_1_2_0170'
 matplotlib_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.2.x of the the python matplotlib package."
diff --git a/test/tool_shed/functional/test_0300_reset_all_metadata.py b/test/shed_functional/functional/test_0300_reset_all_metadata.py
similarity index 99%
rename from test/tool_shed/functional/test_0300_reset_all_metadata.py
rename to test/shed_functional/functional/test_0300_reset_all_metadata.py
index d8e0bc91ccf..1fcf8dfff8f 100644
--- a/test/tool_shed/functional/test_0300_reset_all_metadata.py
+++ b/test/shed_functional/functional/test_0300_reset_all_metadata.py
@@ -1,6 +1,6 @@
 import os
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 datatypes_repository_name = 'emboss_datatypes_0020'
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
diff --git a/test/tool_shed/functional/test_0310_hg_api_features.py b/test/shed_functional/functional/test_0310_hg_api_features.py
similarity index 98%
rename from test/tool_shed/functional/test_0310_hg_api_features.py
rename to test/shed_functional/functional/test_0310_hg_api_features.py
index a10cede4ccf..1aa69fc965b 100644
--- a/test/tool_shed/functional/test_0310_hg_api_features.py
+++ b/test/shed_functional/functional/test_0310_hg_api_features.py
@@ -1,7 +1,7 @@
 import logging
 import os
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_0400_repository_component_reviews.py b/test/shed_functional/functional/test_0400_repository_component_reviews.py
similarity index 99%
rename from test/tool_shed/functional/test_0400_repository_component_reviews.py
rename to test/shed_functional/functional/test_0400_repository_component_reviews.py
index bf7fe710634..960ac5d44bf 100644
--- a/test/tool_shed/functional/test_0400_repository_component_reviews.py
+++ b/test/shed_functional/functional/test_0400_repository_component_reviews.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 repository_name = 'filtering_0400'
 repository_description = 'Galaxy filtering tool for test 0400'
diff --git a/test/tool_shed/functional/test_0410_repository_component_review_access_control.py b/test/shed_functional/functional/test_0410_repository_component_review_access_control.py
similarity index 99%
rename from test/tool_shed/functional/test_0410_repository_component_review_access_control.py
rename to test/shed_functional/functional/test_0410_repository_component_review_access_control.py
index c5873234039..be60d53da07 100644
--- a/test/tool_shed/functional/test_0410_repository_component_review_access_control.py
+++ b/test/shed_functional/functional/test_0410_repository_component_review_access_control.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 repository_name = 'filtering_0410'
 repository_description = 'Galaxy filtering tool for test 0410'
diff --git a/test/tool_shed/functional/test_0420_citable_urls_for_repositories.py b/test/shed_functional/functional/test_0420_citable_urls_for_repositories.py
similarity index 99%
rename from test/tool_shed/functional/test_0420_citable_urls_for_repositories.py
rename to test/shed_functional/functional/test_0420_citable_urls_for_repositories.py
index 6bf1bfe7d8a..5ec84400a1a 100644
--- a/test/tool_shed/functional/test_0420_citable_urls_for_repositories.py
+++ b/test/shed_functional/functional/test_0420_citable_urls_for_repositories.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger(__name__)
 
diff --git a/test/tool_shed/functional/test_0430_browse_utilities.py b/test/shed_functional/functional/test_0430_browse_utilities.py
similarity index 99%
rename from test/tool_shed/functional/test_0430_browse_utilities.py
rename to test/shed_functional/functional/test_0430_browse_utilities.py
index 321a076066c..68672fb808a 100644
--- a/test/tool_shed/functional/test_0430_browse_utilities.py
+++ b/test/shed_functional/functional/test_0430_browse_utilities.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_0440_deleting_dependency_definitions.py b/test/shed_functional/functional/test_0440_deleting_dependency_definitions.py
similarity index 99%
rename from test/tool_shed/functional/test_0440_deleting_dependency_definitions.py
rename to test/shed_functional/functional/test_0440_deleting_dependency_definitions.py
index d43aa28e4eb..7f379c408dc 100644
--- a/test/tool_shed/functional/test_0440_deleting_dependency_definitions.py
+++ b/test/shed_functional/functional/test_0440_deleting_dependency_definitions.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 column_repository_name = 'column_maker_0440'
 column_repository_description = "Add column"
diff --git a/test/tool_shed/functional/test_0450_skip_tool_tests.py b/test/shed_functional/functional/test_0450_skip_tool_tests.py
similarity index 99%
rename from test/tool_shed/functional/test_0450_skip_tool_tests.py
rename to test/shed_functional/functional/test_0450_skip_tool_tests.py
index 364704e70aa..4d2939153ca 100644
--- a/test/tool_shed/functional/test_0450_skip_tool_tests.py
+++ b/test/shed_functional/functional/test_0450_skip_tool_tests.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_0460_upload_to_repository.py b/test/shed_functional/functional/test_0460_upload_to_repository.py
similarity index 99%
rename from test/tool_shed/functional/test_0460_upload_to_repository.py
rename to test/shed_functional/functional/test_0460_upload_to_repository.py
index ac8dc7f9b87..7197378ac85 100644
--- a/test/tool_shed/functional/test_0460_upload_to_repository.py
+++ b/test/shed_functional/functional/test_0460_upload_to_repository.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_0470_tool_dependency_repository_type.py b/test/shed_functional/functional/test_0470_tool_dependency_repository_type.py
similarity index 99%
rename from test/tool_shed/functional/test_0470_tool_dependency_repository_type.py
rename to test/shed_functional/functional/test_0470_tool_dependency_repository_type.py
index fc84170a9d3..216aad64e27 100644
--- a/test/tool_shed/functional/test_0470_tool_dependency_repository_type.py
+++ b/test/shed_functional/functional/test_0470_tool_dependency_repository_type.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py b/test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py
similarity index 98%
rename from test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py
rename to test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py
index 76c732ea79b..015f1752420 100644
--- a/test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py
+++ b/test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_0490_export_import_repositories.py b/test/shed_functional/functional/test_0490_export_import_repositories.py
similarity index 98%
rename from test/tool_shed/functional/test_0490_export_import_repositories.py
rename to test/shed_functional/functional/test_0490_export_import_repositories.py
index 20a3b582e2d..9d5486f2e54 100644
--- a/test/tool_shed/functional/test_0490_export_import_repositories.py
+++ b/test/shed_functional/functional/test_0490_export_import_repositories.py
@@ -1,7 +1,7 @@
 import logging
 import os
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_0500_export_repository_simple_dependency.py b/test/shed_functional/functional/test_0500_export_repository_simple_dependency.py
similarity index 98%
rename from test/tool_shed/functional/test_0500_export_repository_simple_dependency.py
rename to test/shed_functional/functional/test_0500_export_repository_simple_dependency.py
index 366419f0ea7..9dea13db9cb 100644
--- a/test/tool_shed/functional/test_0500_export_repository_simple_dependency.py
+++ b/test/shed_functional/functional/test_0500_export_repository_simple_dependency.py
@@ -1,7 +1,7 @@
 import logging
 import os
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py b/test/shed_functional/functional/test_0510_export_import_repository_complex_dependencies.py
similarity index 98%
rename from test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py
rename to test/shed_functional/functional/test_0510_export_import_repository_complex_dependencies.py
index 90855b28811..e4eed4c0793 100644
--- a/test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py
+++ b/test/shed_functional/functional/test_0510_export_import_repository_complex_dependencies.py
@@ -1,7 +1,7 @@
 import logging
 import os
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_0520_import_export_circular_dependencies.py b/test/shed_functional/functional/test_0520_import_export_circular_dependencies.py
similarity index 98%
rename from test/tool_shed/functional/test_0520_import_export_circular_dependencies.py
rename to test/shed_functional/functional/test_0520_import_export_circular_dependencies.py
index 7f619e97fe1..db641680d3f 100644
--- a/test/tool_shed/functional/test_0520_import_export_circular_dependencies.py
+++ b/test/shed_functional/functional/test_0520_import_export_circular_dependencies.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_0530_repository_admin_feature.py b/test/shed_functional/functional/test_0530_repository_admin_feature.py
similarity index 99%
rename from test/tool_shed/functional/test_0530_repository_admin_feature.py
rename to test/shed_functional/functional/test_0530_repository_admin_feature.py
index 9072959d6be..89e2badd994 100644
--- a/test/tool_shed/functional/test_0530_repository_admin_feature.py
+++ b/test/shed_functional/functional/test_0530_repository_admin_feature.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_0540_get_all_metadata_from_api.py b/test/shed_functional/functional/test_0540_get_all_metadata_from_api.py
similarity index 99%
rename from test/tool_shed/functional/test_0540_get_all_metadata_from_api.py
rename to test/shed_functional/functional/test_0540_get_all_metadata_from_api.py
index 4175b170437..5e4fb20bd09 100644
--- a/test/tool_shed/functional/test_0540_get_all_metadata_from_api.py
+++ b/test/shed_functional/functional/test_0540_get_all_metadata_from_api.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_1000_install_basic_repository.py b/test/shed_functional/functional/test_1000_install_basic_repository.py
similarity index 99%
rename from test/tool_shed/functional/test_1000_install_basic_repository.py
rename to test/shed_functional/functional/test_1000_install_basic_repository.py
index bdde1df1b22..5a65016035d 100644
--- a/test/tool_shed/functional/test_1000_install_basic_repository.py
+++ b/test/shed_functional/functional/test_1000_install_basic_repository.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 
 class BasicToolShedFeatures( ShedTwillTestCase ):
diff --git a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py b/test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
similarity index 99%
rename from test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
rename to test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
index aef9e8e5df3..f3221de8cf1 100644
--- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
+++ b/test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
@@ -1,7 +1,7 @@
 import logging
 import os
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 repository_name = 'freebayes_0010'
 repository_description = "Galaxy's freebayes tool"
diff --git a/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py b/test/shed_functional/functional/test_1020_install_repository_with_repository_dependencies.py
similarity index 99%
rename from test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
rename to test/shed_functional/functional/test_1020_install_repository_with_repository_dependencies.py
index b5b12ac29bc..e43248bdcc3 100644
--- a/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
+++ b/test/shed_functional/functional/test_1020_install_repository_with_repository_dependencies.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 datatypes_repository_name = 'emboss_datatypes_0020'
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
diff --git a/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py b/test/shed_functional/functional/test_1030_install_repository_with_dependency_revisions.py
similarity index 99%
rename from test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
rename to test/shed_functional/functional/test_1030_install_repository_with_dependency_revisions.py
index 5c01205e5d2..47f997ff43b 100644
--- a/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
+++ b/test/shed_functional/functional/test_1030_install_repository_with_dependency_revisions.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 datatypes_repository_name = 'emboss_datatypes_0030'
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
diff --git a/test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py b/test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
similarity index 99%
rename from test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py
rename to test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
index ee47d169eed..02bb7e4a944 100644
--- a/test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py
+++ b/test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 freebayes_repository_name = 'freebayes_0040'
 freebayes_repository_description = "Galaxy's freebayes tool for test 0040"
diff --git a/test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py b/test/shed_functional/functional/test_1050_circular_dependencies_4_levels.py
similarity index 99%
rename from test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py
rename to test/shed_functional/functional/test_1050_circular_dependencies_4_levels.py
index f05bac2d228..41f9e79824f 100644
--- a/test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py
+++ b/test/shed_functional/functional/test_1050_circular_dependencies_4_levels.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 emboss_datatypes_repository_name = 'emboss_datatypes_0050'
 emboss_datatypes_repository_description = "Datatypes for emboss"
diff --git a/test/tool_shed/functional/test_1060_install_repository_with_workflow.py b/test/shed_functional/functional/test_1060_install_repository_with_workflow.py
similarity index 99%
rename from test/tool_shed/functional/test_1060_install_repository_with_workflow.py
rename to test/shed_functional/functional/test_1060_install_repository_with_workflow.py
index 87aef179cb4..c8326458832 100644
--- a/test/tool_shed/functional/test_1060_install_repository_with_workflow.py
+++ b/test/shed_functional/functional/test_1060_install_repository_with_workflow.py
@@ -1,6 +1,6 @@
 import os
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 repository_name = 'filtering_0060'
 repository_description = "Galaxy's filtering tool for test 0060"
diff --git a/test/tool_shed/functional/test_1070_invalid_tool.py b/test/shed_functional/functional/test_1070_invalid_tool.py
similarity index 98%
rename from test/tool_shed/functional/test_1070_invalid_tool.py
rename to test/shed_functional/functional/test_1070_invalid_tool.py
index 822a82d0af3..46edaa76778 100644
--- a/test/tool_shed/functional/test_1070_invalid_tool.py
+++ b/test/shed_functional/functional/test_1070_invalid_tool.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 repository_name = 'bismark_0070'
 repository_description = "Galaxy's bismark wrapper"
diff --git a/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py b/test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
similarity index 99%
rename from test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py
rename to test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
index b40c72e7e71..8598cc941cd 100644
--- a/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py
+++ b/test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 column_repository_name = 'column_maker_0080'
 column_repository_description = "Add column"
diff --git a/test/tool_shed/functional/test_1090_repository_dependency_handling.py b/test/shed_functional/functional/test_1090_repository_dependency_handling.py
similarity index 99%
rename from test/tool_shed/functional/test_1090_repository_dependency_handling.py
rename to test/shed_functional/functional/test_1090_repository_dependency_handling.py
index 045f9901005..5a90f88c2b7 100644
--- a/test/tool_shed/functional/test_1090_repository_dependency_handling.py
+++ b/test/shed_functional/functional/test_1090_repository_dependency_handling.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 column_repository_name = 'column_maker_1085'
 column_repository_description = "Add column"
diff --git a/test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py b/test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py
similarity index 99%
rename from test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py
rename to test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py
index 1004f7c1545..e74f5c475b2 100644
--- a/test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py
+++ b/test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 column_repository_name = 'column_maker_1087'
 column_repository_description = "Add column"
diff --git a/test/tool_shed/functional/test_1110_install_tool_from_tool_search.py b/test/shed_functional/functional/test_1110_install_tool_from_tool_search.py
similarity index 99%
rename from test/tool_shed/functional/test_1110_install_tool_from_tool_search.py
rename to test/shed_functional/functional/test_1110_install_tool_from_tool_search.py
index 6b40ef5374b..8aabb98b0f1 100644
--- a/test/tool_shed/functional/test_1110_install_tool_from_tool_search.py
+++ b/test/shed_functional/functional/test_1110_install_tool_from_tool_search.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 emboss_datatypes_repository_name = 'emboss_datatypes_0090'
 emboss_datatypes_repository_description = "Datatypes for emboss"
diff --git a/test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py b/test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py
similarity index 99%
rename from test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py
rename to test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py
index 4f95d6f8ae6..c6cda4a3d6c 100644
--- a/test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py
+++ b/test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py
@@ -1,6 +1,6 @@
 import os
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 bwa_base_repository_name = 'bwa_base_repository_0100'
 bwa_base_repository_description = "BWA Base"
diff --git a/test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py b/test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py
similarity index 99%
rename from test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py
rename to test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py
index b1d99380da3..c1e5670ac7f 100644
--- a/test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py
+++ b/test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 datatypes_repository_name = 'emboss_datatypes_0110'
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
diff --git a/test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py b/test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
similarity index 99%
rename from test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py
rename to test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
index ce8c78352dc..7757a7215be 100644
--- a/test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py
+++ b/test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 datatypes_repository_name = 'blast_datatypes_0120'
 datatypes_repository_description = 'Galaxy applicable datatypes for BLAST'
diff --git a/test/tool_shed/functional/test_1150_datatype_converters.py b/test/shed_functional/functional/test_1150_datatype_converters.py
similarity index 98%
rename from test/tool_shed/functional/test_1150_datatype_converters.py
rename to test/shed_functional/functional/test_1150_datatype_converters.py
index 0a6fceb74c3..11e5a4b93fa 100644
--- a/test/tool_shed/functional/test_1150_datatype_converters.py
+++ b/test/shed_functional/functional/test_1150_datatype_converters.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 repository_name = 'bed_to_gff_0130'
 repository_description = "Converter: BED to GFF"
diff --git a/test/tool_shed/functional/test_1160_tool_help_images.py b/test/shed_functional/functional/test_1160_tool_help_images.py
similarity index 98%
rename from test/tool_shed/functional/test_1160_tool_help_images.py
rename to test/shed_functional/functional/test_1160_tool_help_images.py
index 56a8f8a491d..ac89fa7f52d 100644
--- a/test/tool_shed/functional/test_1160_tool_help_images.py
+++ b/test/shed_functional/functional/test_1160_tool_help_images.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger(__name__)
 
diff --git a/test/tool_shed/functional/test_1170_prior_installation_required.py b/test/shed_functional/functional/test_1170_prior_installation_required.py
similarity index 99%
rename from test/tool_shed/functional/test_1170_prior_installation_required.py
rename to test/shed_functional/functional/test_1170_prior_installation_required.py
index 6b36c9cb5cf..890c6b739c0 100644
--- a/test/tool_shed/functional/test_1170_prior_installation_required.py
+++ b/test/shed_functional/functional/test_1170_prior_installation_required.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_1180_circular_prior_installation_required.py b/test/shed_functional/functional/test_1180_circular_prior_installation_required.py
similarity index 99%
rename from test/tool_shed/functional/test_1180_circular_prior_installation_required.py
rename to test/shed_functional/functional/test_1180_circular_prior_installation_required.py
index 773f8d72935..6d9d2a80ddb 100644
--- a/test/tool_shed/functional/test_1180_circular_prior_installation_required.py
+++ b/test/shed_functional/functional/test_1180_circular_prior_installation_required.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_1190_complex_prior_installation_required.py b/test/shed_functional/functional/test_1190_complex_prior_installation_required.py
similarity index 99%
rename from test/tool_shed/functional/test_1190_complex_prior_installation_required.py
rename to test/shed_functional/functional/test_1190_complex_prior_installation_required.py
index 69568cdc262..88ecc21e42f 100644
--- a/test/tool_shed/functional/test_1190_complex_prior_installation_required.py
+++ b/test/shed_functional/functional/test_1190_complex_prior_installation_required.py
@@ -1,6 +1,6 @@
 import os
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 matplotlib_repository_name = 'package_matplotlib_1_2_0170'
 matplotlib_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.2.x of the the python matplotlib package."
diff --git a/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py b/test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py
similarity index 99%
rename from test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
rename to test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py
index 558d5900386..b739e305f3d 100644
--- a/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
+++ b/test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 
 class UninstallingAndReinstallingRepositories( ShedTwillTestCase ):
diff --git a/test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py b/test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
similarity index 99%
rename from test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
rename to test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
index 3dbb41eae3e..25ecc3332a5 100644
--- a/test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
+++ b/test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
@@ -1,6 +1,6 @@
 import os
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 
 class UninstallingAndReinstallingRepositories( ShedTwillTestCase ):
diff --git a/test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py b/test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
similarity index 99%
rename from test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
rename to test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
index 3f1a46898bf..fb6a8abe017 100644
--- a/test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
+++ b/test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 datatypes_repository_name = 'emboss_datatypes_0020'
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
diff --git a/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py b/test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
similarity index 99%
rename from test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
rename to test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
index 7b30a306d4c..ba359132df2 100644
--- a/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
+++ b/test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 datatypes_repository_name = 'emboss_datatypes_0030'
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
diff --git a/test/tool_shed/functional/test_1300_reset_all_metadata.py b/test/shed_functional/functional/test_1300_reset_all_metadata.py
similarity index 99%
rename from test/tool_shed/functional/test_1300_reset_all_metadata.py
rename to test/shed_functional/functional/test_1300_reset_all_metadata.py
index 5422493365f..c9aeb5ac190 100644
--- a/test/tool_shed/functional/test_1300_reset_all_metadata.py
+++ b/test/shed_functional/functional/test_1300_reset_all_metadata.py
@@ -1,6 +1,6 @@
 import os
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 datatypes_repository_name = 'emboss_datatypes_0020'
 datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
diff --git a/test/tool_shed/functional/test_1400_review_migration_stages.py b/test/shed_functional/functional/test_1400_review_migration_stages.py
similarity index 97%
rename from test/tool_shed/functional/test_1400_review_migration_stages.py
rename to test/shed_functional/functional/test_1400_review_migration_stages.py
index fd439c2bad9..8499b687be8 100644
--- a/test/tool_shed/functional/test_1400_review_migration_stages.py
+++ b/test/shed_functional/functional/test_1400_review_migration_stages.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 
 class TestToolMigrationStages( ShedTwillTestCase ):
diff --git a/test/tool_shed/functional/test_1410_update_manager.py b/test/shed_functional/functional/test_1410_update_manager.py
similarity index 98%
rename from test/tool_shed/functional/test_1410_update_manager.py
rename to test/shed_functional/functional/test_1410_update_manager.py
index 3d5445fb5c3..20e7171280d 100644
--- a/test/tool_shed/functional/test_1410_update_manager.py
+++ b/test/shed_functional/functional/test_1410_update_manager.py
@@ -1,7 +1,7 @@
 import logging
 import time
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger(__name__)
 
diff --git a/test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py b/test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py
similarity index 99%
rename from test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py
rename to test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py
index 39a1755c815..c01381058df 100644
--- a/test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py
+++ b/test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_1430_repair_installed_repository.py b/test/shed_functional/functional/test_1430_repair_installed_repository.py
similarity index 99%
rename from test/tool_shed/functional/test_1430_repair_installed_repository.py
rename to test/shed_functional/functional/test_1430_repair_installed_repository.py
index b1fa35bddc3..12cfa814056 100644
--- a/test/tool_shed/functional/test_1430_repair_installed_repository.py
+++ b/test/shed_functional/functional/test_1430_repair_installed_repository.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_1440_missing_env_sh_files.py b/test/shed_functional/functional/test_1440_missing_env_sh_files.py
similarity index 99%
rename from test/tool_shed/functional/test_1440_missing_env_sh_files.py
rename to test/shed_functional/functional/test_1440_missing_env_sh_files.py
index b29d8a2cfbc..781297f3ba9 100644
--- a/test/tool_shed/functional/test_1440_missing_env_sh_files.py
+++ b/test/shed_functional/functional/test_1440_missing_env_sh_files.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py b/test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py
similarity index 99%
rename from test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py
rename to test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py
index 5b6227ee929..8aa6cea64e2 100644
--- a/test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py
+++ b/test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py
@@ -1,4 +1,4 @@
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 repository_name = 'proteomics_datatypes_1450'
 repository_description = "Proteomics datatypes"
diff --git a/test/tool_shed/functional/test_1460_data_managers.py b/test/shed_functional/functional/test_1460_data_managers.py
similarity index 98%
rename from test/tool_shed/functional/test_1460_data_managers.py
rename to test/shed_functional/functional/test_1460_data_managers.py
index a59934623c7..f29cf2c5202 100644
--- a/test/tool_shed/functional/test_1460_data_managers.py
+++ b/test/shed_functional/functional/test_1460_data_managers.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger( __name__ )
 
diff --git a/test/tool_shed/functional/test_1470_updating_installed_repositories.py b/test/shed_functional/functional/test_1470_updating_installed_repositories.py
similarity index 99%
rename from test/tool_shed/functional/test_1470_updating_installed_repositories.py
rename to test/shed_functional/functional/test_1470_updating_installed_repositories.py
index cd72d5cafbd..514acf8519d 100644
--- a/test/tool_shed/functional/test_1470_updating_installed_repositories.py
+++ b/test/shed_functional/functional/test_1470_updating_installed_repositories.py
@@ -1,6 +1,6 @@
 import logging
 
-from tool_shed.base.twilltestcase import common, ShedTwillTestCase
+from shed_functional.base.twilltestcase import common, ShedTwillTestCase
 
 log = logging.getLogger(__name__)
 
diff --git a/test/tool_shed/functional_tests.py b/test/shed_functional/functional_tests.py
similarity index 100%
rename from test/tool_shed/functional_tests.py
rename to test/shed_functional/functional_tests.py
diff --git a/test/tool_shed/test_data/0460_files/repository_dependencies.xml b/test/shed_functional/test_data/0460_files/repository_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/0460_files/repository_dependencies.xml
rename to test/shed_functional/test_data/0460_files/repository_dependencies.xml
diff --git a/test/tool_shed/test_data/0460_files/repository_dependencies_in_root.tar b/test/shed_functional/test_data/0460_files/repository_dependencies_in_root.tar
similarity index 100%
rename from test/tool_shed/test_data/0460_files/repository_dependencies_in_root.tar
rename to test/shed_functional/test_data/0460_files/repository_dependencies_in_root.tar
diff --git a/test/tool_shed/test_data/0460_files/repository_dependencies_in_subfolder.tar b/test/shed_functional/test_data/0460_files/repository_dependencies_in_subfolder.tar
similarity index 100%
rename from test/tool_shed/test_data/0460_files/repository_dependencies_in_subfolder.tar
rename to test/shed_functional/test_data/0460_files/repository_dependencies_in_subfolder.tar
diff --git a/test/tool_shed/test_data/0460_files/tool_dependencies.xml b/test/shed_functional/test_data/0460_files/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/0460_files/tool_dependencies.xml
rename to test/shed_functional/test_data/0460_files/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/0460_files/tool_dependencies_in_root.tar b/test/shed_functional/test_data/0460_files/tool_dependencies_in_root.tar
similarity index 100%
rename from test/tool_shed/test_data/0460_files/tool_dependencies_in_root.tar
rename to test/shed_functional/test_data/0460_files/tool_dependencies_in_root.tar
diff --git a/test/tool_shed/test_data/0460_files/tool_dependencies_in_subfolder.tar b/test/shed_functional/test_data/0460_files/tool_dependencies_in_subfolder.tar
similarity index 100%
rename from test/tool_shed/test_data/0460_files/tool_dependencies_in_subfolder.tar
rename to test/shed_functional/test_data/0460_files/tool_dependencies_in_subfolder.tar
diff --git a/test/tool_shed/test_data/0480_files/tool_dependencies.xml b/test/shed_functional/test_data/0480_files/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/0480_files/tool_dependencies.xml
rename to test/shed_functional/test_data/0480_files/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/0540_files/column_maker/column_maker.tar b/test/shed_functional/test_data/0540_files/column_maker/column_maker.tar
similarity index 100%
rename from test/tool_shed/test_data/0540_files/column_maker/column_maker.tar
rename to test/shed_functional/test_data/0540_files/column_maker/column_maker.tar
diff --git a/test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml b/test/shed_functional/test_data/0540_files/column_maker/repository_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml
rename to test/shed_functional/test_data/0540_files/column_maker/repository_dependencies.xml
diff --git a/test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar b/test/shed_functional/test_data/0540_files/convert_chars/convert_chars.tar
similarity index 100%
rename from test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar
rename to test/shed_functional/test_data/0540_files/convert_chars/convert_chars.tar
diff --git a/test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml b/test/shed_functional/test_data/0540_files/convert_chars/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml
rename to test/shed_functional/test_data/0540_files/convert_chars/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml b/test/shed_functional/test_data/0540_files/package_bwa/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml
rename to test/shed_functional/test_data/0540_files/package_bwa/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/1420_files/binary_tarballs/atlas.tar b/test/shed_functional/test_data/1420_files/binary_tarballs/atlas.tar
similarity index 100%
rename from test/tool_shed/test_data/1420_files/binary_tarballs/atlas.tar
rename to test/shed_functional/test_data/1420_files/binary_tarballs/atlas.tar
diff --git a/test/tool_shed/test_data/1420_files/binary_tarballs/boost.tar b/test/shed_functional/test_data/1420_files/binary_tarballs/boost.tar
similarity index 100%
rename from test/tool_shed/test_data/1420_files/binary_tarballs/boost.tar
rename to test/shed_functional/test_data/1420_files/binary_tarballs/boost.tar
diff --git a/test/tool_shed/test_data/1420_files/binary_tarballs/bzlib.tar b/test/shed_functional/test_data/1420_files/binary_tarballs/bzlib.tar
similarity index 100%
rename from test/tool_shed/test_data/1420_files/binary_tarballs/bzlib.tar
rename to test/shed_functional/test_data/1420_files/binary_tarballs/bzlib.tar
diff --git a/test/tool_shed/test_data/1420_files/binary_tarballs/lapack.tar b/test/shed_functional/test_data/1420_files/binary_tarballs/lapack.tar
similarity index 100%
rename from test/tool_shed/test_data/1420_files/binary_tarballs/lapack.tar
rename to test/shed_functional/test_data/1420_files/binary_tarballs/lapack.tar
diff --git a/test/tool_shed/test_data/1420_files/binary_tarballs/numpy.tar b/test/shed_functional/test_data/1420_files/binary_tarballs/numpy.tar
similarity index 100%
rename from test/tool_shed/test_data/1420_files/binary_tarballs/numpy.tar
rename to test/shed_functional/test_data/1420_files/binary_tarballs/numpy.tar
diff --git a/test/tool_shed/test_data/1420_files/binary_tarballs/rdkit.tar b/test/shed_functional/test_data/1420_files/binary_tarballs/rdkit.tar
similarity index 100%
rename from test/tool_shed/test_data/1420_files/binary_tarballs/rdkit.tar
rename to test/shed_functional/test_data/1420_files/binary_tarballs/rdkit.tar
diff --git a/test/tool_shed/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml b/test/shed_functional/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml
rename to test/shed_functional/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml b/test/shed_functional/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml
rename to test/shed_functional/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml b/test/shed_functional/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml
rename to test/shed_functional/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml b/test/shed_functional/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml
rename to test/shed_functional/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml b/test/shed_functional/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml
rename to test/shed_functional/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml b/test/shed_functional/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml
rename to test/shed_functional/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml b/test/shed_functional/test_data/1440_files/complex_dependency/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml
rename to test/shed_functional/test_data/1440_files/complex_dependency/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/1440_files/dependency_definition/tool_dependencies.xml b/test/shed_functional/test_data/1440_files/dependency_definition/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/1440_files/dependency_definition/tool_dependencies.xml
rename to test/shed_functional/test_data/1440_files/dependency_definition/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/1460_files/data_manager_files/test_data_manager.tar b/test/shed_functional/test_data/1460_files/data_manager_files/test_data_manager.tar
similarity index 100%
rename from test/tool_shed/test_data/1460_files/data_manager_files/test_data_manager.tar
rename to test/shed_functional/test_data/1460_files/data_manager_files/test_data_manager.tar
diff --git a/test/tool_shed/test_data/bed_to_gff_converter/bed_to_gff_converter.tar b/test/shed_functional/test_data/bed_to_gff_converter/bed_to_gff_converter.tar
similarity index 100%
rename from test/tool_shed/test_data/bed_to_gff_converter/bed_to_gff_converter.tar
rename to test/shed_functional/test_data/bed_to_gff_converter/bed_to_gff_converter.tar
diff --git a/test/tool_shed/test_data/bismark/bismark.tar b/test/shed_functional/test_data/bismark/bismark.tar
similarity index 100%
rename from test/tool_shed/test_data/bismark/bismark.tar
rename to test/shed_functional/test_data/bismark/bismark.tar
diff --git a/test/tool_shed/test_data/bismark/bismark_methylation_extractor.xml b/test/shed_functional/test_data/bismark/bismark_methylation_extractor.xml
similarity index 100%
rename from test/tool_shed/test_data/bismark/bismark_methylation_extractor.xml
rename to test/shed_functional/test_data/bismark/bismark_methylation_extractor.xml
diff --git a/test/tool_shed/test_data/blast/blast_datatypes.tar b/test/shed_functional/test_data/blast/blast_datatypes.tar
similarity index 100%
rename from test/tool_shed/test_data/blast/blast_datatypes.tar
rename to test/shed_functional/test_data/blast/blast_datatypes.tar
diff --git a/test/tool_shed/test_data/blast/blastxml_to_top_descr.tar b/test/shed_functional/test_data/blast/blastxml_to_top_descr.tar
similarity index 100%
rename from test/tool_shed/test_data/blast/blastxml_to_top_descr.tar
rename to test/shed_functional/test_data/blast/blastxml_to_top_descr.tar
diff --git a/test/tool_shed/test_data/bwa/bwa_base.tar b/test/shed_functional/test_data/bwa/bwa_base.tar
similarity index 100%
rename from test/tool_shed/test_data/bwa/bwa_base.tar
rename to test/shed_functional/test_data/bwa/bwa_base.tar
diff --git a/test/tool_shed/test_data/bwa/bwa_color.tar b/test/shed_functional/test_data/bwa/bwa_color.tar
similarity index 100%
rename from test/tool_shed/test_data/bwa/bwa_color.tar
rename to test/shed_functional/test_data/bwa/bwa_color.tar
diff --git a/test/tool_shed/test_data/bwa/complex/bwa_base.tar b/test/shed_functional/test_data/bwa/complex/bwa_base.tar
similarity index 100%
rename from test/tool_shed/test_data/bwa/complex/bwa_base.tar
rename to test/shed_functional/test_data/bwa/complex/bwa_base.tar
diff --git a/test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml b/test/shed_functional/test_data/bwa/complex/readme/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml
rename to test/shed_functional/test_data/bwa/complex/readme/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/bwa/complex/tool_dependencies.xml b/test/shed_functional/test_data/bwa/complex/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/bwa/complex/tool_dependencies.xml
rename to test/shed_functional/test_data/bwa/complex/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/column_maker/column_maker.tar b/test/shed_functional/test_data/column_maker/column_maker.tar
similarity index 100%
rename from test/tool_shed/test_data/column_maker/column_maker.tar
rename to test/shed_functional/test_data/column_maker/column_maker.tar
diff --git a/test/tool_shed/test_data/convert_chars/convert_chars.tar b/test/shed_functional/test_data/convert_chars/convert_chars.tar
similarity index 100%
rename from test/tool_shed/test_data/convert_chars/convert_chars.tar
rename to test/shed_functional/test_data/convert_chars/convert_chars.tar
diff --git a/test/tool_shed/test_data/emboss/0470_files/emboss_complex_dependency.tar b/test/shed_functional/test_data/emboss/0470_files/emboss_complex_dependency.tar
similarity index 100%
rename from test/tool_shed/test_data/emboss/0470_files/emboss_complex_dependency.tar
rename to test/shed_functional/test_data/emboss/0470_files/emboss_complex_dependency.tar
diff --git a/test/tool_shed/test_data/emboss/0470_files/tool_dependencies.xml b/test/shed_functional/test_data/emboss/0470_files/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/emboss/0470_files/tool_dependencies.xml
rename to test/shed_functional/test_data/emboss/0470_files/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/emboss/datatypes/datatypes_conf.xml b/test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml
similarity index 100%
rename from test/tool_shed/test_data/emboss/datatypes/datatypes_conf.xml
rename to test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml
diff --git a/test/tool_shed/test_data/emboss/emboss.tar b/test/shed_functional/test_data/emboss/emboss.tar
similarity index 100%
rename from test/tool_shed/test_data/emboss/emboss.tar
rename to test/shed_functional/test_data/emboss/emboss.tar
diff --git a/test/tool_shed/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml b/test/shed_functional/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml
rename to test/shed_functional/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml b/test/shed_functional/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml
rename to test/shed_functional/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml b/test/shed_functional/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml
rename to test/shed_functional/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml b/test/shed_functional/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml
rename to test/shed_functional/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/filtering/README b/test/shed_functional/test_data/filtering/README
similarity index 100%
rename from test/tool_shed/test_data/filtering/README
rename to test/shed_functional/test_data/filtering/README
diff --git a/test/tool_shed/test_data/filtering/filtering_0000.txt b/test/shed_functional/test_data/filtering/filtering_0000.txt
similarity index 100%
rename from test/tool_shed/test_data/filtering/filtering_0000.txt
rename to test/shed_functional/test_data/filtering/filtering_0000.txt
diff --git a/test/tool_shed/test_data/filtering/filtering_1.1.0.tar b/test/shed_functional/test_data/filtering/filtering_1.1.0.tar
similarity index 100%
rename from test/tool_shed/test_data/filtering/filtering_1.1.0.tar
rename to test/shed_functional/test_data/filtering/filtering_1.1.0.tar
diff --git a/test/tool_shed/test_data/filtering/filtering_2.2.0.tar b/test/shed_functional/test_data/filtering/filtering_2.2.0.tar
similarity index 100%
rename from test/tool_shed/test_data/filtering/filtering_2.2.0.tar
rename to test/shed_functional/test_data/filtering/filtering_2.2.0.tar
diff --git a/test/tool_shed/test_data/filtering/filtering_test_data.tar b/test/shed_functional/test_data/filtering/filtering_test_data.tar
similarity index 100%
rename from test/tool_shed/test_data/filtering/filtering_test_data.tar
rename to test/shed_functional/test_data/filtering/filtering_test_data.tar
diff --git a/test/tool_shed/test_data/filtering/readme.txt b/test/shed_functional/test_data/filtering/readme.txt
similarity index 100%
rename from test/tool_shed/test_data/filtering/readme.txt
rename to test/shed_functional/test_data/filtering/readme.txt
diff --git a/test/tool_shed/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga b/test/shed_functional/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga
similarity index 100%
rename from test/tool_shed/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga
rename to test/shed_functional/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga
diff --git a/test/tool_shed/test_data/freebayes/freebayes.tar b/test/shed_functional/test_data/freebayes/freebayes.tar
similarity index 100%
rename from test/tool_shed/test_data/freebayes/freebayes.tar
rename to test/shed_functional/test_data/freebayes/freebayes.tar
diff --git a/test/tool_shed/test_data/freebayes/freebayes.xml b/test/shed_functional/test_data/freebayes/freebayes.xml
similarity index 100%
rename from test/tool_shed/test_data/freebayes/freebayes.xml
rename to test/shed_functional/test_data/freebayes/freebayes.xml
diff --git a/test/tool_shed/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml b/test/shed_functional/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml
rename to test/shed_functional/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml b/test/shed_functional/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml
rename to test/shed_functional/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/freebayes/sam_fa_indices.loc.sample b/test/shed_functional/test_data/freebayes/sam_fa_indices.loc.sample
similarity index 100%
rename from test/tool_shed/test_data/freebayes/sam_fa_indices.loc.sample
rename to test/shed_functional/test_data/freebayes/sam_fa_indices.loc.sample
diff --git a/test/tool_shed/test_data/freebayes/tool_data_table_conf.xml.sample b/test/shed_functional/test_data/freebayes/tool_data_table_conf.xml.sample
similarity index 100%
rename from test/tool_shed/test_data/freebayes/tool_data_table_conf.xml.sample
rename to test/shed_functional/test_data/freebayes/tool_data_table_conf.xml.sample
diff --git a/test/tool_shed/test_data/freebayes/tool_dependencies.xml b/test/shed_functional/test_data/freebayes/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/freebayes/tool_dependencies.xml
rename to test/shed_functional/test_data/freebayes/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/htseq_count/htseq_count.tar b/test/shed_functional/test_data/htseq_count/htseq_count.tar
similarity index 100%
rename from test/tool_shed/test_data/htseq_count/htseq_count.tar
rename to test/shed_functional/test_data/htseq_count/htseq_count.tar
diff --git a/test/tool_shed/test_data/package_matplotlib/package_matplotlib_1_2.tar b/test/shed_functional/test_data/package_matplotlib/package_matplotlib_1_2.tar
similarity index 100%
rename from test/tool_shed/test_data/package_matplotlib/package_matplotlib_1_2.tar
rename to test/shed_functional/test_data/package_matplotlib/package_matplotlib_1_2.tar
diff --git a/test/tool_shed/test_data/package_matplotlib/tool_dependencies.xml b/test/shed_functional/test_data/package_matplotlib/tool_dependencies.xml
similarity index 100%
rename from test/tool_shed/test_data/package_matplotlib/tool_dependencies.xml
rename to test/shed_functional/test_data/package_matplotlib/tool_dependencies.xml
diff --git a/test/tool_shed/test_data/package_numpy/package_numpy_1_7.tar b/test/shed_functional/test_data/package_numpy/package_numpy_1_7.tar
similarity index 100%
rename from test/tool_shed/test_data/package_numpy/package_numpy_1_7.tar
rename to test/shed_functional/test_data/package_numpy/package_numpy_1_7.tar
diff --git a/test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar b/test/shed_functional/test_data/proteomics_datatypes/proteomics_datatypes.tar
similarity index 100%
rename from test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar
rename to test/shed_functional/test_data/proteomics_datatypes/proteomics_datatypes.tar
diff --git a/test/tool_shed/test_data/readme.txt b/test/shed_functional/test_data/readme.txt
similarity index 100%
rename from test/tool_shed/test_data/readme.txt
rename to test/shed_functional/test_data/readme.txt
diff --git a/test/tool_shed/test_data/repository_capsules/0490_filtering.tar.gz b/test/shed_functional/test_data/repository_capsules/0490_filtering.tar.gz
similarity index 100%
rename from test/tool_shed/test_data/repository_capsules/0490_filtering.tar.gz
rename to test/shed_functional/test_data/repository_capsules/0490_filtering.tar.gz
diff --git a/test/tool_shed/test_data/repository_capsules/0500_emboss_5.tar.gz b/test/shed_functional/test_data/repository_capsules/0500_emboss_5.tar.gz
similarity index 100%
rename from test/tool_shed/test_data/repository_capsules/0500_emboss_5.tar.gz
rename to test/shed_functional/test_data/repository_capsules/0500_emboss_5.tar.gz
diff --git a/test/tool_shed/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz b/test/shed_functional/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz
similarity index 100%
rename from test/tool_shed/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz
rename to test/shed_functional/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz
diff --git a/test/tool_shed/test_data/repository_capsules/0520_filtering.tar.gz b/test/shed_functional/test_data/repository_capsules/0520_filtering.tar.gz
similarity index 100%
rename from test/tool_shed/test_data/repository_capsules/0520_filtering.tar.gz
rename to test/shed_functional/test_data/repository_capsules/0520_filtering.tar.gz
diff --git a/test/unit/tool_shed_unit_tests/__init__.py b/test/unit/shed_unit/__init__.py
similarity index 100%
rename from test/unit/tool_shed_unit_tests/__init__.py
rename to test/unit/shed_unit/__init__.py
diff --git a/test/unit/tool_shed_unit_tests/test_fabric_util.py b/test/unit/shed_unit/test_fabric_util.py
similarity index 100%
rename from test/unit/tool_shed_unit_tests/test_fabric_util.py
rename to test/unit/shed_unit/test_fabric_util.py
diff --git a/test/unit/tool_shed_unit_tests/test_td_common_util.py b/test/unit/shed_unit/test_td_common_util.py
similarity index 100%
rename from test/unit/tool_shed_unit_tests/test_td_common_util.py
rename to test/unit/shed_unit/test_td_common_util.py
diff --git a/test/unit/tool_shed_unit_tests/test_tool_panel_manager.py b/test/unit/shed_unit/test_tool_panel_manager.py
similarity index 100%
rename from test/unit/tool_shed_unit_tests/test_tool_panel_manager.py
rename to test/unit/shed_unit/test_tool_panel_manager.py