force defaults to always print

python/scripts/run_gubbins.py

@@ -28,24 +28,24 @@
 
 
 
-parser = argparse.ArgumentParser(description='Croucher N. J., Page A. J., Connor T. R., Delaney A. J., Keane J. A., Bentley S. D., Parkhill J., Harris S.R. "Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins". Nucleic Acids Res. 2015 Feb 18;43(3):e15. doi: 10.1093/nar/gku1196 .')
+parser = argparse.ArgumentParser(description='Croucher N. J., Page A. J., Connor T. R., Delaney A. J., Keane J. A., Bentley S. D., Parkhill J., Harris S.R. "Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins". Nucleic Acids Res. 2015 Feb 18;43(3):e15. doi: 10.1093/nar/gku1196 .', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 parser.add_argument('alignment_filename', help='Multifasta alignment file')
 parser.add_argument('--outgroup', '-o', help='Outgroup name for rerooting. A list of comma separated names can be used if they form a clade')
 parser.add_argument('--starting_tree', '-s', help='Starting tree')
 parser.add_argument('--use_time_stamp', '-u', action='count', help='Use a time stamp in file names', default = 0)
 parser.add_argument('--verbose', '-v', action='count', help='Turn on debugging', default = 0)
 parser.add_argument('--no_cleanup', '-n', action='count', help='Dont cleanup intermediate files', default = 0)
-parser.add_argument('--tree_builder', '-t', help='Application to use for tree building [raxml|fasttree|hybrid], default RAxML', default = "raxml")
-parser.add_argument('--iterations', '-i', help='Maximum No. of iterations, default is 5', type=int, default = 5)
-parser.add_argument('--min_snps', '-m', help='Min SNPs to identify a recombination block, default is 3', type=int, default = 3)
-parser.add_argument('--filter_percentage','-f', help='Filter out taxa with more than this percentage of gaps, default is 25', type=int, default = 25)
+parser.add_argument('--tree_builder', '-t', help='Application to use for tree building [raxml|fasttree|hybrid]', default = "raxml")
+parser.add_argument('--iterations', '-i', help='Maximum No. of iterations', type=int, default = 5)
+parser.add_argument('--min_snps', '-m', help='Min SNPs to identify a recombination block', type=int, default = 3)
+parser.add_argument('--filter_percentage','-f', help='Filter out taxa with more than this percentage of gaps', type=int, default = 25)
 parser.add_argument('--prefix', '-p', help='Add a prefix to the final output filenames')
 parser.add_argument('--threads', '-c', help='Number of threads to run with RAXML, but only if a PTHREADS version is available', type=int, default = 1)
 parser.add_argument('--converge_method', '-z', help='Criteria to use to know when to halt iterations [weighted_robinson_foulds|robinson_foulds|recombination]', default = 'weighted_robinson_foulds')
 parser.add_argument('--version', action='version', version=str(pkg_resources.get_distribution("gubbins").version))
-parser.add_argument('--min_window_size', '-a', help='Minimum window size, default 100', type=int, default = 100)
-parser.add_argument('--max_window_size', '-b', help='Maximum window size, default 10000', type=int, default = 10000)
-parser.add_argument('--raxml_model', '-r', help='RAxML model [GTRGAMMA|GTRCAT], default GTRCAT', default = 'GTRCAT')
+parser.add_argument('--min_window_size', '-a', help='Minimum window size', type=int, default = 100)
+parser.add_argument('--max_window_size', '-b', help='Maximum window size', type=int, default = 10000)
+parser.add_argument('--raxml_model', '-r', help='RAxML model [GTRGAMMA|GTRCAT]', default = 'GTRCAT')
 parser.add_argument('--remove_identical_sequences', '-d', action='count', help='Remove identical sequences', default = 0)
 
 gubbins_runner = common.GubbinsCommon(parser.parse_args())