diff --git a/test-data/1.sam.gz b/test-data/1.sam.gz
new file mode 100644
index 00000000000..542e9b365b7
Binary files /dev/null and b/test-data/1.sam.gz differ
diff --git a/test-data/bad.html.gz b/test-data/bad.html.gz
new file mode 100644
index 00000000000..b1fc23ff07d
Binary files /dev/null and b/test-data/bad.html.gz differ
diff --git a/test-data/random-file b/test-data/random-file
new file mode 100644
index 00000000000..9f53451616d
Binary files /dev/null and b/test-data/random-file differ
diff --git a/test/functional/tools/sample_datatypes_conf.xml b/test/functional/tools/sample_datatypes_conf.xml
index 0431842db02..75e562603b9 100644
--- a/test/functional/tools/sample_datatypes_conf.xml
+++ b/test/functional/tools/sample_datatypes_conf.xml
@@ -24,5 +24,6 @@
     <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true"/>
     <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="true" />
     <datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" type_extension="bgzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
   </registration>
 </datatypes>
diff --git a/test/integration/test_upload_configuration_options.py b/test/integration/test_upload_configuration_options.py
new file mode 100644
index 00000000000..c006b667897
--- /dev/null
+++ b/test/integration/test_upload_configuration_options.py
@@ -0,0 +1,129 @@
+"""Integration tests various upload aspects.
+
+This file checks upload options that require different non-default Galaxy
+configuration options. More vanilla upload options and behaviors are tested
+with the API test framework (located in test_tools.py).
+
+These options include:
+ - The config optiond check_upload_content and allow_path_paste.
+ - The upload API parameter auto_decompress.
+ - Checking for malicious content in uploads of compressed files.
+ - Restricting file:// uploads to admins and allowing them only when
+   allow_path_paste is set to True.
+"""
+
+import os
+
+from base import integration_util
+from base.populators import DatasetPopulator
+
+SCRIPT_DIR = os.path.normpath(os.path.dirname(__file__))
+TEST_DATA_DIRECTORY = os.path.join(SCRIPT_DIR, os.pardir, os.pardir, "test-data")
+
+
+class BaseCheckUploadContentConfigurationTestCase(integration_util.IntegrationTestCase):
+
+    framework_tool_and_types = True
+
+    def setUp(self):
+        super(BaseCheckUploadContentConfigurationTestCase, self).setUp()
+        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        self.history_id = self.dataset_populator.new_history()
+
+
+class NonAdminsCannotPasteFilePathTestCase(BaseCheckUploadContentConfigurationTestCase):
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["allow_path_paste"] = True
+
+    def test(self):
+        payload = self.dataset_populator.upload_payload(
+            self.history_id, 'file://%s/1.RData' % TEST_DATA_DIRECTORY, ext="binary"
+        )
+        create_response = self._post( "tools", data=payload )
+        # Ideally this would be 403 but the tool API endpoint isn't using
+        # the newer API decorator that handles those details.
+        assert create_response.status_code >= 400
+
+
+class AdminsCanPasteFilePathsTestCase(BaseCheckUploadContentConfigurationTestCase):
+
+    require_admin_user = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["allow_path_paste"] = True
+
+    def test(self):
+        payload = self.dataset_populator.upload_payload(
+            self.history_id, 'file://%s/random-file' % TEST_DATA_DIRECTORY,
+        )
+        create_response = self._post( "tools", data=payload )
+        # Ideally this would be 403 but the tool API endpoint isn't using
+        # the newer API decorator that handles those details.
+        assert create_response.status_code == 200
+
+
+class DefaultBinaryContentFiltersTestCase(BaseCheckUploadContentConfigurationTestCase):
+
+    require_admin_user = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["allow_path_paste"] = True
+
+    def test_random_binary_allowed(self):
+        dataset = self.dataset_populator.new_dataset(
+            self.history_id, 'file://%s/random-file' % TEST_DATA_DIRECTORY, file_type="auto", wait=True
+        )
+        dataset = self.dataset_populator.get_history_dataset_details(self.history_id, dataset=dataset)
+        assert dataset["file_ext"] == "data", dataset
+
+    def test_gzipped_html_content_blocked_by_default(self):
+        dataset = self.dataset_populator.new_dataset(
+            self.history_id, 'file://%s/bad.html.gz' % TEST_DATA_DIRECTORY, file_type="auto", wait=True
+        )
+        dataset = self.dataset_populator.get_history_dataset_details(self.history_id, dataset=dataset)
+        assert dataset["file_size"] == 0
+
+
+class DisableContentCheckingTestCase(BaseCheckUploadContentConfigurationTestCase):
+
+    require_admin_user = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["allow_path_paste"] = True
+        config["check_upload_content"] = False
+
+    def test_gzipped_html_content_now_allowed(self):
+        dataset = self.dataset_populator.new_dataset(
+            self.history_id, 'file://%s/bad.html.gz' % TEST_DATA_DIRECTORY, file_type="auto", wait=True
+        )
+        dataset = self.dataset_populator.get_history_dataset_details(self.history_id, dataset=dataset)
+        # Same file was empty above!
+        assert dataset["file_size"] != 0
+
+
+class AutoDecompressTestCase(BaseCheckUploadContentConfigurationTestCase):
+
+    require_admin_user = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["allow_path_paste"] = True
+
+    def test_auto_decompress_off(self):
+        dataset = self.dataset_populator.new_dataset(
+            self.history_id, 'file://%s/1.sam.gz' % TEST_DATA_DIRECTORY, file_type="auto", auto_decompress=False, wait=True
+        )
+        dataset = self.dataset_populator.get_history_dataset_details(self.history_id, dataset=dataset)
+        assert dataset["file_ext"] == "data", dataset
+
+    def test_auto_decompress_on(self):
+        dataset = self.dataset_populator.new_dataset(
+            self.history_id, 'file://%s/1.sam.gz' % TEST_DATA_DIRECTORY, file_type="auto", wait=True
+        )
+        dataset = self.dataset_populator.get_history_dataset_details(self.history_id, dataset=dataset)
+        assert dataset["file_ext"] == "sam", dataset