Mercurial > repos > rliterman > csp2

comparison CSP2/bin/chooseRefs.py @ 27:792274118b2e

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"planemo upload"
author rliterman
date Wed, 04 Dec 2024 12:50:59 -0500
parents 01431fa12065
children 893a6993efe3
comparison
equal deleted inserted replaced
26:6f85641ecd48 27:792274118b2e
81 break 81 break
82 82
83 return [file_path,contig_count,assembly_bases,n50,n90,l50,l90] 83 return [file_path,contig_count,assembly_bases,n50,n90,l50,l90]
84 84
85 parser = argparse.ArgumentParser(description='Choose reference isolates based on FASTA metrics and mean distances.') 85 parser = argparse.ArgumentParser(description='Choose reference isolates based on FASTA metrics and mean distances.')
86 parser.add_argument('--ref_count', type=int, help='Number of reference isolates to select') 86 parser.add_argument('--ref_count', type=int, default=1, help='Number of reference isolates to select')
87 parser.add_argument('--mash_triangle_file', type=str, help='Path to the mash triangle file') 87 parser.add_argument('--mash_triangle_file', type=str, help='Path to the mash triangle file')
88 parser.add_argument('--trim_name', type=str, help='Trim name') 88 parser.add_argument('--trim_name', type=str, default="", help='trim name')
89 args = parser.parse_args() 89 args = parser.parse_args()
90 90
91 ref_count = args.ref_count 91 ref_count = args.ref_count
92 mash_triangle_file = os.path.abspath(args.mash_triangle_file) 92 mash_triangle_file = os.path.abspath(args.mash_triangle_file)
93 trim_name = args.trim_name 93 trim_name = args.trim_name