clades: Add validation options

This keeps consistent with other subcommands that take node data JSON as
input.

augur/clades.py

@@ -22,6 +22,7 @@
 from .io.file import PANDAS_READ_CSV_OPTIONS
 from argparse import SUPPRESS
 from .utils import get_parent_name_by_child_name_for_tree, read_node_data, write_json, get_json_name
+from .argparse_ import add_validation_arguments
 
 UNASSIGNED = 'unassigned'
 
@@ -324,10 +325,10 @@ def get_reference_sequence_from_root_node(all_muts, root_name):
 
     return ref
 
-def parse_nodes(tree_file, node_data_files):
+def parse_nodes(tree_file, node_data_files, validation_mode):
     tree = Phylo.read(tree_file, 'newick')
     # don't supply tree to read_node_data as we don't want to require that every node is present in the node_data JSONs
-    node_data = read_node_data(node_data_files)
+    node_data = read_node_data(node_data_files, validation_mode=validation_mode)
     # node_data files can be parsed without 'nodes' (if they have 'branches')
     if "nodes" not in node_data or len(node_data['nodes'].keys())==0:
         raise AugurError(f"No nodes found in the supplied node data files. Please check {', '.join(node_data_files)}")
@@ -347,11 +348,12 @@ def register_parser(parent_subparsers):
     parser.add_argument('--output-node-data', type=str,  metavar="NODE_DATA_JSON", help='name of JSON file to save clade assignments to')
     parser.add_argument('--membership-name', type=str, default="clade_membership", help='Key to store clade membership under; use "None" to not export this')
     parser.add_argument('--label-name', type=str, default="clade", help='Key to store clade labels under; use "None" to not export this')
+    add_validation_arguments(parser)
     return parser
 
 
 def run(args):
-    (tree, all_muts) = parse_nodes(args.tree, args.mutations)
+    (tree, all_muts) = parse_nodes(args.tree, args.mutations, args.validation_mode)
 
     if args.reference:
         # PLACE HOLDER FOR vcf WORKFLOW.