diff --git a/lib/galaxy/model/tags.py b/lib/galaxy/model/tags.py
index 6192b25ba53..14e73d67784 100644
--- a/lib/galaxy/model/tags.py
+++ b/lib/galaxy/model/tags.py
@@ -311,6 +311,8 @@ class TagHandler(object):
     def _get_name_value_pair(self, tag_str):
         """Get name, value pair from a tag string."""
         # Use regular expression to parse name, value.
+        if tag_str.startswith('#'):
+            tag_str = "name:%s" % tag_str[1:]
         reg_exp = re.compile("[" + self.key_value_separators + "]")
         name_value_pair = reg_exp.split(tag_str, 1)
         # Add empty slot if tag does not have value.
diff --git a/lib/galaxy/tools/relabel_from_file.xml b/lib/galaxy/tools/relabel_from_file.xml
index e60457b90ea..c35cb51de74 100644
--- a/lib/galaxy/tools/relabel_from_file.xml
+++ b/lib/galaxy/tools/relabel_from_file.xml
@@ -147,6 +147,9 @@
         in the collection. In that case only matching list identifiers will be
         relabeled.
 
+        Valid identifiers must contain only characters (a-z, A-Z), numbers (0-9), 
+        dash and underscore (-, _). Punctuation or whitespace are not allowed. 
+
         This tool will create new history datasets from your collection
         but your quota usage will not increase.
     ]]></help>
diff --git a/lib/galaxy/tools/tag_collection_from_file.xml b/lib/galaxy/tools/tag_collection_from_file.xml
index 1427fb504c5..2abad0f5452 100644
--- a/lib/galaxy/tools/tag_collection_from_file.xml
+++ b/lib/galaxy/tools/tag_collection_from_file.xml
@@ -34,13 +34,13 @@
                     <assert_contents>
                         <has_text_matching expression="^This is a line of text.\n$" />
                     </assert_contents>
-                    <metadata name="tags" value="alias:f,alias:r1,orientation:forward,zoo" />
+                    <metadata name="tags" value="alias:f,alias:r1,name:forward,orientation:forward,zoo" />
                 </element>
                 <element name="reverse">
                     <assert_contents>
                         <has_text_matching expression="^This is a different line of text.\n$" />
                     </assert_contents>
-                    <metadata name="tags" value="alias:r,alias:r2,orientation:reverse" />
+                    <metadata name="tags" value="alias:r,alias:r2,name:reverse,orientation:reverse" />
                 </element>
             </output_collection>
         </test>
@@ -63,13 +63,13 @@
                         <assert_contents>
                             <has_text_matching expression="^This is a line of text.\n$" />
                         </assert_contents>
-                        <metadata name="tags" value="alias:f,alias:r1,orientation:forward" />
+                        <metadata name="tags" value="alias:f,alias:r1,name:forward,orientation:forward" />
                     </element>
                     <element name="reverse">
                         <assert_contents>
                             <has_text_matching expression="^This is a different line of text.\n$" />
                         </assert_contents>
-                        <metadata name="tags" value="alias:r,alias:r2,orientation:reverse" />
+                        <metadata name="tags" value="alias:r,alias:r2,name:reverse,orientation:reverse" />
                     </element>
                 </element>
             </output_collection>
diff --git a/test-data/new_tags_1.txt b/test-data/new_tags_1.txt
index 91caa6c4fae..4dbd9d7a001 100644
--- a/test-data/new_tags_1.txt
+++ b/test-data/new_tags_1.txt
@@ -1,2 +1,2 @@
-forward	orientation:forward	alias:r1	alias:f
-reverse	orientation:reverse	alias:r2	alias:r
+forward	orientation:forward	alias:r1	alias:f	#forward
+reverse	orientation:reverse	alias:r2	alias:r	#reverse