diff --git a/doc/source/dev/data_managers.rst b/doc/source/dev/data_managers.rst
index 6b0737e4d17..7320385f75b 100644
--- a/doc/source/dev/data_managers.rst
+++ b/doc/source/dev/data_managers.rst
@@ -101,6 +101,8 @@ This tag defines a particular Data Manager. Any number of
 +---------------+------------+-----------+--------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | ``id``        | A string*  | no        | ``id="twobit_builder"``                          | Must be unique across all Data Managers; should be lowercase and contain only letters, numbers, and underscores. While technically optional, it is a best-practice to specify this value. When not specified, it will use the id of the underlying Data Manager Tool. |
 +---------------+------------+-----------+--------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| ``version``   | A string*  | no        | ``version="0.0.1"``                              | Deprecated with release 21.09. The version of the data manager defaults to the version of the data manager tool                                                                                                                                                       |
++---------------+------------+-----------+--------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 
 The following is an example that contains all of the attributes
 described above.
@@ -616,7 +618,7 @@ the ``extra_files_path`` of ``out_file``.
 
 .. code-block:: xml
 
-    <tool id="data_manager_fetch_genome_all_fasta" name="Reference Genome" version="0.0.1" tool_type="manage_data">
+    <tool id="data_manager_fetch_genome_all_fasta" name="Reference Genome" tool_type="manage_data">
         <description>fetching</description>
         <command interpreter="python">data_manager_fetch_genome_all_fasta.py "${out_file}" --dbkey_description ${ dbkey.get_display_text() }</command>
         <inputs>
diff --git a/lib/galaxy/tools/data_manager/manager.py b/lib/galaxy/tools/data_manager/manager.py
index 25f9f89214b..e26425d10b5 100644
--- a/lib/galaxy/tools/data_manager/manager.py
+++ b/lib/galaxy/tools/data_manager/manager.py
@@ -140,7 +140,6 @@ class DataManager:
         self.declared_id = elem.get('id')
         self.guid = elem.get('guid')
         path = elem.get('tool_file')
-        self.version = elem.get('version', self.version)
         tool_shed_repository = None
         tool_guid = None
 
@@ -169,6 +168,7 @@ class DataManager:
         self.name = elem.get('name', self.tool.name)
         self.description = elem.get('description', self.tool.description)
         self.undeclared_tables = util.asbool(elem.get('undeclared_tables', self.undeclared_tables))
+        self.version = elem.get('version', self.tool.version)
 
         for data_table_elem in elem.findall('data_table'):
             data_table_name = data_table_elem.get("name")
diff --git a/scripts/fix_dm_versions.py b/scripts/fix_dm_versions.py
new file mode 100755
index 00000000000..0983e305505
--- /dev/null
+++ b/scripts/fix_dm_versions.py
@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+import argparse
+import shutil
+from datetime import datetime
+
+from lxml import etree
+
+desc = """
+Fix shed_data_manager_conf.xml
+
+Modifies the guid and version attribute of data_manager tags:
+
+- the version in the guid (text after the last slash) is replaced
+  by the data manager tool version
+- the version attribute is set to the data manager tool version
+
+By default only data managers with duplicated guid are modified
+and version attributes are not added if absent.
+
+A copy of the original file with a time stamp appended to the name
+is created.
+
+Note, if there are versions of the data manager tool that have the
+same version there will still be DMs with duplicated guids. These
+need to be corrected manually.
+"""
+
+parser = argparse.ArgumentParser(description=desc)
+parser.add_argument('shed_data_manager_conf', metavar='CONFIG_FILE', type=str,
+                    default="config/shed_data_manager_conf.xml",
+                    help='an integer for the accumulator')
+parser.add_argument('--all-entries', action='store_true',
+                    help='modify all entries (default only those with duplicated guid)')
+parser.add_argument('--add-version', action='store_true',
+                    help='also add version attribute if absent')
+parser.add_argument('--dry-run', action='store_true',
+                    help='do not write resulting config file')
+args = parser.parse_args()
+
+with open(args.shed_data_manager_conf) as fh:
+    tree = etree.parse(args.shed_data_manager_conf)
+root = tree.getroot()
+
+guid_mapping = dict()
+for dm in root.iter('data_manager'):
+    guid = dm.attrib["guid"]
+    if guid not in guid_mapping:
+        guid_mapping[guid] = [dm]
+    else:
+        guid_mapping[guid].append(dm)
+
+for guid in guid_mapping:
+    if len(guid_mapping[guid]) > 1:
+        print(f'{guid} found {len(guid_mapping[guid])}x')
+    elif not args.all_entries:
+        continue
+
+    for dm in guid_mapping[guid]:
+        tool_version = dm.find("./tool/version")
+        tool_version = tool_version.text
+
+        new_guid = f"{guid[:guid.rfind('/')]}/{tool_version}"
+        dm.attrib['guid'] = new_guid
+        print(f"changing guid: {guid} -> {new_guid}")
+        if "version" in dm.attrib:
+            print(f"changing version: {dm.attrib['version']} -> {tool_version}")
+            dm.attrib['version'] = tool_version
+        elif args.add_version:
+            print(f"adding version: {tool_version}")
+            dm.attrib['version'] = tool_version
+
+if not args.dry_run:
+    nfn = args.shed_data_manager_conf + datetime.now().isoformat()
+    print(f"save copy at {nfn}")
+    shutil.copyfile(args.shed_data_manager_conf, nfn)
+    print(f"saving {args.shed_data_manager_conf}")
+    tree.write(args.shed_data_manager_conf)