--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/tagdust_architecture_data_manager.py	Sun May 08 04:44:17 2016 -0400
@@ -0,0 +1,113 @@
+#!/usr/bin/env python
+
+import json
+import optparse
+import os.path
+
+def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
+    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+    data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
+    data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
+    return data_manager_dict
+
+
+def get_param(name, params, default=None,  check_tab=True):
+    value = params.get(name)
+    print name, value
+    return check_param(name, value, default=default, check_tab=check_tab)
+
+
+def check_param(name, value, default=None,  check_tab=True):
+    if value in [ None, '', '?' ]:
+        if default:
+            print "Using {0} for {1} as no value provided".format( default, name )
+            value = default
+        else:
+            raise Exception( '{0} is not a valid {1}. You must specify a valid {1}.'.format( value, name ) )
+    if check_tab and "\t" in value:
+        raise Exception( '{0} is not a valid {1}. It may not contain a tab because these are used as seperators by galaxy .'.format( value, name ) )
+    return value
+
+
+def createFileBasedOnHmm(hmms):
+    file_name = ""
+    bar_code = "no"
+    for hmm in hmms:
+        block = hmm["block"].strip()
+        if not (block[0] in ['R','O','G','B','F','S','P']):
+            raise Exception( "hmm block {0} is not a valid. It must start with one of  ['R','O','G','B','F','S','P'].".format( block ) )
+        if block[0] == 'B':
+            bar_code = "yes"
+        if block[1] != ':':
+            raise Exception( "hmm block {0} is not a valid. The second character must be ':'".format( block ) )
+        if "\t" in hmm:
+            raise Exception( "hmm block {0} is not a valid. It may not contain a tab, due to galaxy using tabs as seperators".format( block ) )
+        file_name = file_name + block + "_"
+    file_name = file_name[:-1] + ".txt"
+    return bar_code, file_name
+
+
+def get_path(galaxy_tool_dir, file_name):
+    file_path =  os.path.join(galaxy_tool_dir, "tagdust_architecture")
+    if os.path.exists(file_path):
+        if os.path.isfile(file_path):
+            raise Exception( "Found a file at {0}, but expecting a directory there".format( file_path ) )
+    else:
+        os.mkdir(file_path)
+    return os.path.join(file_path, file_name)
+
+
+def writeHmm(hmms, file_path):
+    with open( file_path, 'w' ) as output_file:
+        output_file.write("./tagdust") 
+        for i, hmm in enumerate( hmms, 1 ):
+            output_file.write(" ")
+            output_file.write(str(-i))
+            output_file.write(" ")
+            output_file.write(hmm["block"])
+        output_file.write("\n")
+
+def main():
+
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '--data_table_name', action='store', type="string", default=None, help='path' )
+    parser.add_option( '--json_output_file', action='store', type="string", default=None, help='path' )
+    (options, args) = parser.parse_args()
+
+    data_table_name = check_param("data_table_name", options.data_table_name)
+    json_output_file = check_param("json_output_file", options.json_output_file, check_tab=False)
+
+    param_dict = json.loads( open( json_output_file ).read() )
+    params = param_dict.get("param_dict")
+    print "input params:"
+    print params
+
+    hmms = get_param("hmms", params)
+    galaxy_tool_dir = get_param("GALAXY_DATA_INDEX_DIR", params)
+
+    data_table_entry = {}
+
+    data_table_entry["barcode"], file_name = createFileBasedOnHmm(hmms)
+    data_table_entry["path"] =  get_path(galaxy_tool_dir, file_name)
+    writeHmm(hmms, data_table_entry["path"])
+
+    basename = os.path.basename(data_table_entry["path"])
+    filename = os.path.splitext(basename)[0]
+    data_table_entry["name"] = get_param("name", params, default=filename)
+    data_table_entry["value"] = get_param("value", params, default=data_table_entry["name"])
+    data_table_entry["dbkey"] = get_param("dbkey", params, default=data_table_entry["value"])
+
+    data_manager_dict = {}
+    _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
+
+    print "output:"
+    print data_manager_dict
+    # save info to json file
+    with open( json_output_file, 'wb' ) as output_file:
+        output_file.write( json.dumps( data_manager_dict ) )
+        output_file.write( "\n" )
+
+
+if __name__ == "__main__": 
+    main()