Typo in help message: '_' instead of '-'

[evolarjun]

The error message: amrrules: error: You must specify --input, --output_prefix, and --organism (or --organism_file) unless using --download-resources. has '_' in --output_prefix and --organism_file, when in the message above it looks like they should be --output-prefix and --organism-file.

Example when forgetting to include an --output-prefix:

$ amrrules --input test_kpneumo_disrupt.tsv --organism 's__Klebsiella pneumoniae'
usage: amrrules [-h] [--input INPUT] [--output-prefix OUTPUT_PREFIX] [--output-dir OUTPUT_DIR]
                [--sample-id SAMPLE_ID]
                [--organism ORGANISM | --organism-file ORGANISM_FILE | --list-organisms]
                [--amr-tool AMR_TOOL] [--no-rule-interpretation {nwtR,nwtS,nwt,none}]
                [--annot-opts {minimal,full}] [--flag-core] [--full-disrupt] [--print-non-amr]
                [--download-resources] [--version]
amrrules: error: You must specify --input, --output_prefix, and --organism (or --organism_file) unless using --download-resources.

--output_prefix doesn't work:

$ amrrules --input test_kpneumo_disrupt.tsv --organism 's__Klebsiella pneumoniae' --output_prefix test
usage: amrrules [-h] [--input INPUT] [--output-prefix OUTPUT_PREFIX] [--output-dir OUTPUT_DIR]
                [--sample-id SAMPLE_ID]
                [--organism ORGANISM | --organism-file ORGANISM_FILE | --list-organisms]
                [--amr-tool AMR_TOOL] [--no-rule-interpretation {nwtR,nwtS,nwt,none}]
                [--annot-opts {minimal,full}] [--flag-core] [--full-disrupt] [--print-non-amr]
                [--download-resources] [--version]
amrrules: error: unrecognized arguments: --output_prefix test

--output-prefix does:

$ amrrules --input test_kpneumo_disrupt.tsv --organism 's__Klebsiella pneumoniae' --output-prefix test
20 hits matched a rule and 73 hits did not match a rule.
Output written to /netmnt/vast01/gp/home/aprasad/src/AMRrules/tests/data/input/test_interpreted.tsv.
Summary output written to /netmnt/vast01/gp/home/aprasad/src/AMRrules/tests/data/input/test_genome_summary.tsv.