diff --git a/config/tool_conf.xml.sample b/config/tool_conf.xml.sample
index 581bca8e16d2..890a6f1a183e 100644
--- a/config/tool_conf.xml.sample
+++ b/config/tool_conf.xml.sample
@@ -36,10 +36,10 @@
     <tool file="${model_tools_path}/filter_failed_collection.xml" />
     <tool file="${model_tools_path}/flatten_collection.xml" />
     <tool file="${model_tools_path}/merge_collection.xml" />
-    <tool file="${model_tools_path}/tag_collection_from_file.xml" />
     <tool file="${model_tools_path}/relabel_from_file.xml" />
     <tool file="${model_tools_path}/filter_from_file.xml" />
     <tool file="${model_tools_path}/sort_collection_list.xml" />
+    <tool file="${model_tools_path}/tag_collection_from_file.xml" />
   </section>
   <section id="liftOver" name="Lift-Over">
     <tool file="extract/liftOver_wrapper.xml" />
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index cc1500b8c876..db471241b614 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2611,7 +2611,7 @@ class TagFromFileTool(DatabaseOperationTool):
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         hdca = incoming["input"]
-        set_tags = incoming['set_tags']
+        how = incoming['how']
         new_tags_dataset_assoc = incoming["tags"]
         new_elements = odict()
         tags_manager = GalaxyTagManager(trans.app.model.context)
@@ -2624,10 +2624,13 @@ def add_copied_value_to_new_elements(new_tags_dict, dce):
                 history.add_dataset(copied_value, copied_value, set_hid=False)
                 new_tags = new_tags_dict.get(dce.element_identifier)
                 if new_tags:
-                    if not set_tags and dce.element_object.tags:
+                    if how in ('add', 'remove') and dce.element_object.tags:
                         # We need get the original tags and update them with the new tags
                         old_tags = set(tag for tag in tags_manager.get_tags_str(dce.element_object.tags).split(',') if tag)
-                        old_tags.update(set(new_tags))
+                        if how == 'add':
+                            old_tags.update(set(new_tags))
+                        elif how == 'remove':
+                            old_tags = old_tags - set(new_tags)
                         new_tags = old_tags
                     tags_manager.add_tags_from_list(user=history.user, item=copied_value, new_tags_list=new_tags)
             else:
@@ -2638,10 +2641,13 @@ def add_copied_value_to_new_elements(new_tags_dict, dce):
                     # don't set `visible` to `False` if you don't hide the original elements.
                     new_element.element_object.visible = False
                     new_tags = new_tags_dict.get(new_element.element_identifier)
-                    if not set_tags:
+                    if how in ('add', 'remove'):
                         old_tags = set(tag for tag in tags_manager.get_tags_str(old_element.element_object.tags).split(',') if tag)
                         if new_tags:
-                            old_tags.update(set(new_tags))
+                            if how == 'add':
+                                old_tags.update(set(new_tags))
+                            elif how == 'remove':
+                                old_tags = old_tags - set(new_tags)
                         new_tags = old_tags
                     tags_manager.add_tags_from_list(user=history.user, item=new_element.element_object, new_tags_list=new_tags)
             new_elements[dce.element_identifier] = copied_value
diff --git a/lib/galaxy/tools/tag_collection_from_file.xml b/lib/galaxy/tools/tag_collection_from_file.xml
index 497b16fd003b..3666a386c415 100644
--- a/lib/galaxy/tools/tag_collection_from_file.xml
+++ b/lib/galaxy/tools/tag_collection_from_file.xml
@@ -8,8 +8,12 @@
             class="ModelOperationToolAction"/>
     <inputs>
         <param type="data_collection" name="input" label="Input Collection" help="A tabular file indicating how to tag collection elements."/>
-           <param type="data" name="tags" format="tabular" label="Add tags from this file" />
-        <param name="set_tags" type="boolean" label="Set tags instead of updating tags?" help="If you select yes existing tags will be removed, otherwise new tags and existing tags will be merged."/>
+        <param type="data" name="tags" format="tabular" label="Tag collection elements according to this file"/>
+        <param name="how" type="select" label="How should the tags be updated">
+            <option value="add">New tags will be added, existing tags will be kept</option>
+            <option value="set">New tags will be added, existing tags will be removed</option>
+            <option value="remove">The tags listed will be removed</option>
+        </param>
     </inputs>
     <outputs>
         <collection name="output" format_source="input" type_source="input" label="${on_string} (Tagged)" >
@@ -24,18 +28,19 @@
                 </collection>
             </param>
             <param name="tags" value="new_tags_1.txt" ftype="txt" />
+            <param name="how" value="add"/>
             <output_collection name="output" type="list">
                 <element name="forward">
-                  <assert_contents>
-                    <has_text_matching expression="^This is a line of text.\n$" />
-                  </assert_contents>
-                  <metadata name="tags" value="alias:r1,orientation:forward" />
+                    <assert_contents>
+                        <has_text_matching expression="^This is a line of text.\n$" />
+                    </assert_contents>
+                    <metadata name="tags" value="alias:r1,orientation:forward" />
                 </element>
                 <element name="reverse">
-                  <assert_contents>
-                    <has_text_matching expression="^This is a different line of text.\n$" />
-                  </assert_contents>
-                  <metadata name="tags" value="alias:r2,orientation:reverse" />
+                    <assert_contents>
+                        <has_text_matching expression="^This is a different line of text.\n$" />
+                    </assert_contents>
+                    <metadata name="tags" value="alias:r2,orientation:reverse" />
                 </element>
             </output_collection>
         </test>
@@ -50,22 +55,23 @@
                     </element>
                 </collection>
             </param>
+            <param name="how" value="set"/>
             <param name="tags" value="new_tags_1.txt" ftype="txt" />
             <output_collection name="output" type="list:paired">
-              <element name="i1">
-                <element name="forward">
-                  <assert_contents>
-                    <has_text_matching expression="^This is a line of text.\n$" />
-                  </assert_contents>
-                  <metadata name="tags" value="alias:r1,orientation:forward" />
-                </element>
-                <element name="reverse">
-                  <assert_contents>
-                    <has_text_matching expression="^This is a different line of text.\n$" />
-                  </assert_contents>
-                  <metadata name="tags" value="alias:r2,orientation:reverse" />
+                <element name="i1">
+                    <element name="forward">
+                        <assert_contents>
+                            <has_text_matching expression="^This is a line of text.\n$" />
+                        </assert_contents>
+                        <metadata name="tags" value="alias:r1,orientation:forward" />
+                    </element>
+                    <element name="reverse">
+                        <assert_contents>
+                            <has_text_matching expression="^This is a different line of text.\n$" />
+                        </assert_contents>
+                        <metadata name="tags" value="alias:r2,orientation:reverse" />
+                    </element>
                 </element>
-              </element>
             </output_collection>
         </test>
     </tests>