diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 076452e941b..728ef0952ea 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1852,7 +1852,7 @@ class History(HasTags, Dictifiable, UsesAnnotations, HasName, RepresentById):
             hdas = self.active_datasets
         for hda in hdas:
             # Copy HDA.
-            new_hda = hda.copy(force_flush=False)
+            new_hda = hda.copy(flush=False)
             new_history.add_dataset(new_hda, set_hid=False, quota=applies_to_quota)
 
             if target_user:
@@ -3110,7 +3110,7 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
             self.version = self.version + 1 if self.version else 1
             session.add(past_hda)
 
-    def copy(self, parent_id=None, copy_tags=None, force_flush=True, copy_hid=True, new_name=None):
+    def copy(self, parent_id=None, copy_tags=None, flush=True, copy_hid=True, new_name=None):
         """
         Create a copy of this HDA.
         """
@@ -3147,7 +3147,7 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
                 object_session(self).flush([self])
 
             hda.set_peek()
-        if force_flush:
+        if flush:
             object_session(self).flush()
         return hda
 
@@ -4120,7 +4120,7 @@ class DatasetCollection(Dictifiable, UsesAnnotations, RepresentById):
         error_message = "Dataset collection has no %s with key %s." % (get_by_attribute, key)
         raise KeyError(error_message)
 
-    def copy(self, destination=None, element_destination=None):
+    def copy(self, destination=None, element_destination=None, flush=True):
         new_collection = DatasetCollection(
             collection_type=self.collection_type,
             element_count=self.element_count
@@ -4130,6 +4130,7 @@ class DatasetCollection(Dictifiable, UsesAnnotations, RepresentById):
                 new_collection,
                 destination=destination,
                 element_destination=element_destination,
+                flush=flush
             )
         object_session(self).add(new_collection)
         object_session(self).flush()
@@ -4537,16 +4538,17 @@ class DatasetCollectionElement(Dictifiable, RepresentById):
         else:
             return [element_object]
 
-    def copy_to_collection(self, collection, destination=None, element_destination=None):
+    def copy_to_collection(self, collection, destination=None, element_destination=None, flush=True):
         element_object = self.element_object
         if element_destination:
             if self.is_collection:
                 element_object = element_object.copy(
                     destination=destination,
-                    element_destination=element_destination
+                    element_destination=element_destination,
+                    flush=flush
                 )
             else:
-                new_element_object = element_object.copy()
+                new_element_object = element_object.copy(flush=flush)
                 if destination is not None and element_object.hidden_beneath_collection_instance:
                     new_element_object.hidden_beneath_collection_instance = destination
                 # Ideally we would not need to give the following
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 44cd161b217..5363ecedecb 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2902,7 +2902,7 @@ class MergeCollectionTool(DatabaseOperationTool):
         new_elements = OrderedDict()
         for key, value in new_element_structure.items():
             if getattr(value, "history_content_type", None) == "dataset":
-                copied_value = value.copy(force_flush=False)
+                copied_value = value.copy(flush=False)
             else:
                 copied_value = value.copy()
             new_elements[key] = copied_value
@@ -2920,7 +2920,7 @@ class FilterDatasetsTool(DatabaseOperationTool):
         for dce in elements_to_copy:
             element_identifier = dce.element_identifier
             if getattr(dce.element_object, "history_content_type", None) == "dataset":
-                copied_value = dce.element_object.copy(force_flush=False)
+                copied_value = dce.element_object.copy(flush=False)
             else:
                 copied_value = dce.element_object.copy()
             new_elements[element_identifier] = copied_value
@@ -2995,7 +2995,7 @@ class FlattenTool(DatabaseOperationTool):
                 if dce.is_collection:
                     add_elements(dce_object, prefix=identifier)
                 else:
-                    copied_dataset = dce_object.copy(force_flush=False)
+                    copied_dataset = dce_object.copy(flush=False)
                     new_elements[identifier] = copied_dataset
                     copied_datasets.append(copied_dataset)
 
@@ -3041,7 +3041,7 @@ class SortTool(DatabaseOperationTool):
 
         for dce in sorted_elements:
             dce_object = dce.element_object
-            copied_dataset = dce_object.copy(force_flush=False)
+            copied_dataset = dce_object.copy(flush=False)
             new_elements[dce.element_identifier] = copied_dataset
 
         self._add_datasets_to_history(history, itervalues(new_elements))
@@ -3065,7 +3065,7 @@ class RelabelFromFileTool(DatabaseOperationTool):
             if new_label in new_elements:
                 raise Exception("New identifier [%s] appears twice in resulting collection, these values must be unique." % new_label)
             if getattr(dce_object, "history_content_type", None) == "dataset":
-                copied_value = dce_object.copy(force_flush=False)
+                copied_value = dce_object.copy(flush=False)
             else:
                 copied_value = dce_object.copy()
             new_elements[new_label] = copied_value
@@ -3111,7 +3111,7 @@ class ApplyRulesTool(DatabaseOperationTool):
         copied_datasets = []
 
         def copy_dataset(dataset):
-            copied_dataset = dataset.copy(force_flush=False)
+            copied_dataset = dataset.copy(flush=False)
             copied_datasets.append(copied_dataset)
             return copied_dataset
 
@@ -3137,7 +3137,7 @@ class TagFromFileTool(DatabaseOperationTool):
 
         def add_copied_value_to_new_elements(new_tags_dict, dce):
             if getattr(dce.element_object, "history_content_type", None) == "dataset":
-                copied_value = dce.element_object.copy(force_flush=False)
+                copied_value = dce.element_object.copy(flush=False)
                 # copy should never be visible, since part of a collection
                 copied_value.visble = False
                 new_datasets.append(copied_value)
@@ -3208,7 +3208,7 @@ class FilterFromFileTool(DatabaseOperationTool):
             passes_filter = in_filter_file if how_filter == "remove_if_absent" else not in_filter_file
 
             if getattr(dce_object, "history_content_type", None) == "dataset":
-                copied_value = dce_object.copy(force_flush=False)
+                copied_value = dce_object.copy(flush=False)
             else:
                 copied_value = dce_object.copy()
 
diff --git a/lib/galaxy/tools/sort_collection_list.xml b/lib/galaxy/tools/sort_collection_list.xml
index 7c8d3467a52..52256326364 100644
--- a/lib/galaxy/tools/sort_collection_list.xml
+++ b/lib/galaxy/tools/sort_collection_list.xml
@@ -7,7 +7,7 @@
     <action module="galaxy.tools.actions.model_operations"
             class="ModelOperationToolAction"/>
     <inputs>
-        <param type="data_collection" collection_type="list" name="input" label="Input Collection" />
+        <param type="data_collection" collection_type="list,list:paired" name="input" label="Input Collection" />
         <conditional name="sort_type">
             <param type="select" name="sort_type" label="Sort collection identifiers" help="All element identifiers must be present once.">
                 <option value="alpha">alphabetically</option>
@@ -22,7 +22,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <collection name="output" format_source="input" type="list" label="${on_string} (sorted)" >
+        <collection name="output" format_source="input" type_source="input" label="${on_string} (sorted)" >
         </collection>
     </outputs>
     <tests>
@@ -91,6 +91,51 @@
                 </element>
             </output_collection>
         </test>
+        <test>
+            <param name="input">
+                <collection type="list:paired">
+                    <element name="def456">
+                        <collection type="paired">
+                            <element name="forward" value="simple_line.txt" />
+                            <element name="reverse" value="simple_line_alternative.txt" />
+                        </collection>
+                    </element>
+                    <element name="abc789">
+                        <collection type="paired">
+                            <element name="forward" value="simple_line.txt" />
+                            <element name="reverse" value="simple_line_alternative.txt" />
+                        </collection>
+                    </element>
+                </collection>
+            </param>
+            <param name="sort_type" value="alpha" />
+            <output_collection name="output" type="list:paired">
+                <element name="abc789">
+                    <element name="forward">
+                        <assert_contents>
+                            <has_text_matching expression="^This is a line of text.\n$" />
+                        </assert_contents>
+                    </element>
+                    <element name="reverse">
+                        <assert_contents>
+                            <has_text_matching expression="^This is a different line of text.\n$" />
+                        </assert_contents>
+                    </element>
+                </element>
+                <element name="def456">
+                    <element name="forward">
+                        <assert_contents>
+                            <has_text_matching expression="^This is a line of text.\n$" />
+                        </assert_contents>
+                    </element>
+                    <element name="reverse">
+                        <assert_contents>
+                            <has_text_matching expression="^This is a different line of text.\n$" />
+                        </assert_contents>
+                    </element>
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[