diff --git a/data_managers/data_manager_groot_database_downloader/data_manager/data_manager_groot_database_downloader.py b/data_managers/data_manager_groot_database_downloader/data_manager/data_manager_groot_database_downloader.py
new file mode 100644
index 00000000000..baa8aeda007
--- /dev/null
+++ b/data_managers/data_manager_groot_database_downloader/data_manager/data_manager_groot_database_downloader.py
@@ -0,0 +1,149 @@
+#!/usr/bin/env python
+#
+# Data manager for reference data for the MetaPhlAn Galaxy tools
+import argparse
+import json
+import shutil
+import subprocess
+from datetime import date
+from pathlib import Path
+
+
+# Utility functions for interacting with Galaxy JSON
+def read_input_json(json_fp):
+ """Read the JSON supplied from the data manager tool
+ Returns a tuple (param_dict,extra_files_path)
+ 'param_dict' is an arbitrary dictionary of parameters
+ input into the tool; 'extra_files_path' is the path
+ to a directory where output files must be put for the
+ receiving data manager to pick them up.
+ NB the directory pointed to by 'extra_files_path'
+ doesn't exist initially, it is the job of the script
+ to create it if necessary.
+ """
+ with open(json_fp) as fh:
+ params = json.load(fh)
+ return (params['param_dict'],
+ Path(params['output_data'][0]['extra_files_path']))
+
+
+# Utility functions for creating data table dictionaries
+#
+# Example usage:
+# >>> d = create_data_tables_dict()
+# >>> add_data_table(d,'my_data')
+# >>> add_data_table_entry(dict(dbkey='hg19',value='human'))
+# >>> add_data_table_entry(dict(dbkey='mm9',value='mouse'))
+# >>> print(json.dumps(d))
+def create_data_tables_dict():
+ """Return a dictionary for storing data table information
+ Returns a dictionary that can be used with 'add_data_table'
+ and 'add_data_table_entry' to store information about a
+ data table. It can be converted to JSON to be sent back to
+ the data manager.
+ """
+ d = {
+ 'data_tables': {}
+ }
+ return d
+
+
+def add_data_table(d, table):
+ """Add a data table to the data tables dictionary
+ Creates a placeholder for a data table called 'table'.
+ """
+ d['data_tables'][table] = []
+
+
+def add_data_table_entry(d, table, entry):
+ """Add an entry to a data table
+ Appends an entry to the data table 'table'. 'entry'
+ should be a dictionary where the keys are the names of
+ columns in the data table.
+ Raises an exception if the named data table doesn't
+ exist.
+ """
+ try:
+ d['data_tables'][table].append(entry)
+ except KeyError:
+ raise Exception("add_data_table_entry: no table '%s'" % table)
+
+
+def download_groot_db(data_tables, name, table_name, target_dp, identity, groot_version):
+ """Download GROOT database
+ Creates references to the specified file(s) on the Galaxy
+ server in the appropriate data table (determined from the
+ file extension).
+ The 'data_tables' dictionary should have been created using
+ the 'create_data_tables_dict' and 'add_data_table' functions.
+ Arguments:
+ data_tables: a dictionary containing the data table info
+ name: name of the database to download
+ table_name: name of the table
+ target_dp: directory to put copy or link to the data file
+ identity: identity threshold for GROOT
+ groot_version: version of GROOT to use
+ """
+ # Build the command string
+ cmd = "groot get -d %s -o %s --identity %s" % (name, Path.cwd(), identity)
+
+ # Execute the command
+ subprocess.check_call(cmd, shell=True)
+
+ # Define the target directory path
+ current_db_dp = Path(f"{Path.cwd()}/{name}.{identity}")
+ new_db_dp = Path(f"{target_dp}/{name}.{identity}")
+ shutil.copytree(current_db_dp, new_db_dp)
+
+ # Add the data table entry
+ add_data_table_entry(
+ data_tables,
+ table_name,
+ dict(
+ value='%s.%s' % (name, identity),
+ name='%s (%s percent identity)' % (name, identity),
+ path='/%s.%s' % (name, identity),
+ version=groot_version
+ )
+ )
+
+
+if __name__ == "__main__":
+ print("Starting...")
+
+ # Read command line
+ parser = argparse.ArgumentParser(description='Download and build Groot database')
+ parser.add_argument('--database', help="Name of the database")
+ parser.add_argument('--percentidentity', help="The identity threshold at which the database was clustered")
+ parser.add_argument('--grootversion', help="Version of the Database")
+ parser.add_argument('--json', help="Path to JSON file")
+ args = parser.parse_args()
+ print("args : %s" % args)
+
+ # Read the input JSON
+ json_fp = Path(args.json)
+ params, target_dp = read_input_json(json_fp)
+
+ # Make the target directory
+ print("Making %s" % target_dp)
+ target_dp.mkdir(parents=True, exist_ok=True)
+
+ # Set up data tables dictionary
+ data_tables = create_data_tables_dict()
+ add_data_table(data_tables, "groot_database")
+
+ # Fetch data from specified data sources
+ print("Download and build database")
+ download_groot_db(
+ data_tables,
+ args.database,
+ "groot_database",
+ target_dp,
+ args.percentidentity,
+ args.grootversion)
+
+ # Write output JSON
+ print("Outputting JSON")
+ with open(json_fp, 'w') as fh:
+ json.dump(data_tables, fh, sort_keys=True)
+ print("Done.")
\ No newline at end of file
diff --git a/data_managers/data_manager_groot_database_downloader/data_manager/data_manager_groot_database_downloader.xml b/data_managers/data_manager_groot_database_downloader/data_manager/data_manager_groot_database_downloader.xml
index 03740dfb1a4..1e6d1ae2568 100644
--- a/data_managers/data_manager_groot_database_downloader/data_manager/data_manager_groot_database_downloader.xml
+++ b/data_managers/data_manager_groot_database_downloader/data_manager/data_manager_groot_database_downloader.xml
@@ -11,26 +11,13 @@
groot
-
-
-
-
diff --git a/data_managers/data_manager_groot_database_downloader/test-data/groot_database.loc b/data_managers/data_manager_groot_database_downloader/test-data/groot_database.loc
index db085db56f4..36e0e9fd63c 100644
--- a/data_managers/data_manager_groot_database_downloader/test-data/groot_database.loc
+++ b/data_managers/data_manager_groot_database_downloader/test-data/groot_database.loc
@@ -4,3 +4,6 @@ arg-annot.90 arg-annot (90 percent identity) /tmp/tmp7wrj6zk0/galaxy-dev/tool-da
arg-annot.90 arg-annot (90 percent identity) /tmp/tmpf4g2mbca/galaxy-dev/tool-data/groot_database/data/arg-annot.90 1.1.2
arg-annot.90 arg-annot (90 percent identity) /tmp/tmppzyeuezs/galaxy-dev/tool-data/groot_database/arg-annot.90 1.1.2
arg-annot.90 arg-annot (90 percent identity) /tmp/tmpk61hkg7b/galaxy-dev/tool-data/groot_database/data/arg-annot.90 1.1.2
+arg-annot.90 arg-annot (90 percent identity) /tmp/tmpuh2hc68n/galaxy-dev/tool-data/groot_database/data/arg-annot.90 1.1.2
+arg-annot.90 arg-annot (90 percent identity) /tmp/tmpr3ytm5sp/galaxy-dev/tool-data/groot_database/data/arg-annot.90 1.1.2
+arg-annot.90 arg-annot (90 percent identity) /tmp/tmpgktyt4ga/galaxy-dev/tool-data/groot_database/data/arg-annot.90 1.1.2