Commit d078bf61 authored by VIGNET Pierre's avatar VIGNET Pierre
Browse files

[cmd] Clarify model_file argument

parent 0b48ac00
......@@ -352,7 +352,8 @@ def main():
help=solutions_search.__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser_input_file.add_argument('model_file')
parser_input_file.add_argument('model_file',
help="Cadbiom model (.bcx file).")
# Get final_property alone OR an input_file containing multiple properties
group = parser_input_file.add_mutually_exclusive_group(required=True)
group.add_argument('final_prop', nargs='?',
......@@ -411,7 +412,7 @@ def main():
help=solutions_2_graphs.__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser_trajectories.add_argument('model_file',
help="bcx model file.")
help="Cadbiom model (.bcx file).")
parser_trajectories.add_argument('path',
help="Complete solution file or directory with MAC solutions files "
"(*mac_complete.txt files) generated with the 'compute_macs' command.")
......@@ -429,7 +430,7 @@ def main():
help=queries_2_json.__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser_queries_2_json.add_argument('model_file',
help="bcx model file.")
help="Cadbiom model (.bcx file).")
parser_queries_2_json.add_argument('path',
help="Complete solution file or directory with MAC solutions files "
"(*mac_complete.txt files) generated with the 'compute_macs' command.")
......@@ -471,7 +472,7 @@ def main():
help=queries_2_common_graph.__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser_trajectories.add_argument('model_file',
help="bcx model file.")
help="Cadbiom model (.bcx file).")
parser_trajectories.add_argument('path',
help="Complete solution file or directory with MAC solutions files "
"(*mac_complete.txt files) generated with the 'compute_macs' command.")
......@@ -498,7 +499,7 @@ def main():
help=queries_2_occcurrence_matrix.__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser_occurrences_matrix.add_argument('model_file',
help="bcx model file.")
help="Cadbiom model (.bcx file).")
parser_occurrences_matrix.add_argument('path',
help="Directory with MAC solutions files "
"(*mac.txt files) generated with the 'compute_macs' command.")
......@@ -536,7 +537,7 @@ def main():
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser_model_identifier_mapping.add_argument('model_file',
help="bcx model file.")
help="Cadbiom model (.bcx file).")
group = parser_model_identifier_mapping.add_mutually_exclusive_group(required=True)
group.add_argument('--external_file',
help="File with 1 external identifiers to be mapped per line."
......@@ -555,9 +556,9 @@ def main():
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser_model_comparison.add_argument('model_file_1',
help="bcx model file.")
help="Cadbiom model (.bcx file).")
parser_model_comparison.add_argument('model_file_2',
help="bcx model file.")
help="Cadbiom model (.bcx file).")
# Export graphs for the 2 models; default: false
parser_model_comparison.add_argument('--graphs', action='store_true',
help="Create two GraphML files from the given models.")
......@@ -576,7 +577,8 @@ def main():
help=model_info.__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser_model_info.add_argument('model_file')
parser_model_info.add_argument('model_file',
help="Cadbiom model (.bcx file).")
# Filters
group = parser_model_info.add_mutually_exclusive_group(required=True)
# PS: Argparse doesn't allow to select a default value here
......@@ -612,7 +614,8 @@ def main():
help=model_graph.__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser_model_graph.add_argument('model_file')
parser_model_graph.add_argument('model_file',
help="Cadbiom model (.bcx file).")
# Additional data
parser_model_graph.add_argument('--centralities', action='store_true',
help="Get centralities for each node of the graph "
......
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