Mercurial > repos > iuc > vsnp_determine_ref_from_data

comparison vsnp_get_snps.py @ 5:a8560decb495 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
author iuc
date Tue, 16 Nov 2021 20:12:56 +0000
parents e3016c6c5994
children 532a11cdd818
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4:e3016c6c5994 5:a8560decb495
438 if __name__ == '__main__': 438 if __name__ == '__main__':
439 439
440 parser = argparse.ArgumentParser() 440 parser = argparse.ArgumentParser()
441 441
442 parser.add_argument('--ac', action='store', dest='ac', type=int, help='Allele count value'), 442 parser.add_argument('--ac', action='store', dest='ac', type=int, help='Allele count value'),
443 parser.add_argument('--all_isolates', action='store_true', dest='all_isolates', required=False, default=False, help='Create table with all isolates'), 443 parser.add_argument('--all_isolates', action='store_true', dest='all_isolates', help='Create table with all isolates'),
444 parser.add_argument('--input_excel', action='store', dest='input_excel', required=False, default=None, help='Optional Excel filter file'), 444 parser.add_argument('--input_excel', action='store', dest='input_excel', required=False, default=None, help='Optional Excel filter file'),
445 parser.add_argument('--input_vcf_dir', action='store', dest='input_vcf_dir', help='Input vcf directory'), 445 parser.add_argument('--input_vcf_dir', action='store', dest='input_vcf_dir', help='Input vcf directory'),
446 parser.add_argument('--min_mq', action='store', dest='min_mq', type=int, help='Minimum map quality value'), 446 parser.add_argument('--min_mq', action='store', dest='min_mq', type=int, help='Minimum map quality value'),
447 parser.add_argument('--min_quality_score', action='store', dest='min_quality_score', type=int, help='Minimum quality score value'), 447 parser.add_argument('--min_quality_score', action='store', dest='min_quality_score', type=int, help='Minimum quality score value'),
448 parser.add_argument('--output_json_avg_mq_dir', action='store', dest='output_json_avg_mq_dir', help='Output json average mq directory'), 448 parser.add_argument('--output_json_avg_mq_dir', action='store', dest='output_json_avg_mq_dir', help='Output json average mq directory'),