Mercurial > repos > rliterman > csp2
diff CSP2/bin/screenSNPDiffs.py @ 27:792274118b2e
"planemo upload"
author | rliterman |
---|---|
date | Wed, 04 Dec 2024 12:50:59 -0500 |
parents | 01431fa12065 |
children | 893a6993efe3 |
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--- a/CSP2/bin/screenSNPDiffs.py Tue Dec 03 16:35:35 2024 -0500 +++ b/CSP2/bin/screenSNPDiffs.py Wed Dec 04 12:50:59 2024 -0500 @@ -548,17 +548,17 @@ parser = argparse.ArgumentParser() parser.add_argument("--snpdiffs_file", help="Path to the file containing SNP diffs") parser.add_argument("--log_dir", help="Path to the log directory") -parser.add_argument("--min_cov", type=float, help="Minimum coverage") -parser.add_argument("--min_len", type=int, help="Minimum length") -parser.add_argument("--min_iden", type=float, help="Minimum identity") -parser.add_argument("--ref_edge", type=int, help="Reference edge") -parser.add_argument("--query_edge", type=int, help="Query edge") -parser.add_argument("--density_windows", help="Density windows (comma-separated)") -parser.add_argument("--max_snps", help="Maximum SNPs (comma-separated)") -parser.add_argument("--trim_name", help="Trim name") +parser.add_argument("--min_cov", default=85, type=float, help="Minimum coverage") +parser.add_argument("--min_len", default=500,type=int, help="Minimum length") +parser.add_argument("--min_iden", default=99,type=float, help="Minimum identity") +parser.add_argument("--ref_edge", default=150,type=int, help="Reference edge") +parser.add_argument("--query_edge", default=150,type=int, help="Query edge") +parser.add_argument("--density_windows",default="1000,125,15", help="Density windows (comma-separated)") +parser.add_argument("--max_snps", default="3,2,1",help="Maximum SNPs (comma-separated)") +parser.add_argument('--trim_name', type=str, default="", help='trim name') parser.add_argument("--output_file", help="Output file") parser.add_argument("--ref_id", help="Reference IDs file") -parser.add_argument("--tmp_dir", help="TMP dir") +parser.add_argument("--tmp_dir",default="", help="TMP dir") args = parser.parse_args()