add parameter metainfo_reconcile

panX.py

@@ -29,6 +29,8 @@
     help='run specific steps or run all steps by default', metavar='')
 parser.add_argument('-mo', '--metainfo_organism', action='store_true',
     help='add organism information in metadata table.')
+parser.add_argument('-mr', '--metainfo_reconcile', action='store_true',
+    help='use reconciled metadata (redundancy removed) instead of original metadata.')
 parser.add_argument('-rt', '--raxml_max_time', type = int, default = 30,
     help='RAxML tree optimization: maximal runing time (minutes, default:30min)' , metavar='')
 parser.add_argument('-t', '--threads', type = int, default = 1,
@@ -181,6 +183,7 @@
     gbk_present=params.gbk_present,
     threads=params.threads,
     metainfo_organism=params.metainfo_organism,
+    metainfo_reconcile=params.metainfo_reconcile,
     raxml_max_time=params.raxml_max_time,
     blast_fpath=params.blast_file_path,
     roary_fpath=params.roary_file_path,