wrangle_tree - CLI interface

A tool to wrangle phylogenetic trees as needed for processing.

wrangle_tree [-h] [--config_file CONFIG_FILE] [--log_filename LOG_FILENAME] [--log_console]
             [-r REPORT_FILENAME]
             tree_filename {newick,nexus} wrangler_configuration_file out_tree_filename
             {newick,nexus}

wrangle_tree positional arguments

• tree_filename - Path to phylogenetic tree. (default: None)

• tree_schema - The schema of the input phylogenetic tree. (default: None)

• wrangler_configuration_file - Path to phylogenetic tree wrangler configuration. (default: None)

• out_tree_filename - Path to write the wrangled phylogenetic tree. (default: None)

• out_tree_schema - The schema of the output phylogenetic tree. (default: None)

wrangle_tree optional arguments

• -h, --help - show this help message and exit

• --config_file CONFIG_FILE - Path to configuration file. (default: None)

• --log_filename LOG_FILENAME, -l LOG_FILENAME - A file location to write logging data. (default: None)

• --log_console - If provided, write log to console.

• -r REPORT_FILENAME, --report_filename REPORT_FILENAME - Path to write report. (default: None)