Mercurial > repos > mheinzl > variant_analyzer2
comparison read2mut.py @ 42:da224c392a54 draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Wed, 24 Feb 2021 14:20:17 +0000 |
| parents | db3ed9202516 |
| children | d21960b45a6b |
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| 41:db3ed9202516 | 42:da224c392a54 |
|---|---|
| 58 parser.add_argument('--thresh', type=int, default=0, | 58 parser.add_argument('--thresh', type=int, default=0, |
| 59 help='Integer threshold for displaying mutations. Only mutations occuring less than thresh times are displayed. Default of 0 displays all.') | 59 help='Integer threshold for displaying mutations. Only mutations occuring less than thresh times are displayed. Default of 0 displays all.') |
| 60 parser.add_argument('--phred', type=int, default=20, | 60 parser.add_argument('--phred', type=int, default=20, |
| 61 help='Integer threshold for Phred score. Only reads higher than this threshold are considered. Default 20.') | 61 help='Integer threshold for Phred score. Only reads higher than this threshold are considered. Default 20.') |
| 62 parser.add_argument('--trim5', type=int, default=10, | 62 parser.add_argument('--trim5', type=int, default=10, |
| 63 help='Integer threshold for assigning mutations at start of reads to lower tier. Default 10.') | 63 help='Integer threshold for assigning mutations at the beginning of the reads to lower tier. Default 10.') |
| 64 parser.add_argument('--trim3', type=int, default=10, | 64 parser.add_argument('--trim3', type=int, default=10, |
| 65 help='Integer threshold for assigning mutations at end of reads to lower tier. Default 10.') | 65 help='Integer threshold for assigning mutations at the end of the reads to lower tier. Default 10.') |
| 66 parser.add_argument('--chimera_correction', action="store_true", | 66 parser.add_argument('--chimera_correction', action="store_true", |
| 67 help='Count chimeric variants and correct the variant frequencies') | 67 help='Count chimeric variants and correct the variant frequencies') |
| 68 return parser | 68 return parser |
| 69 | 69 |
| 70 | 70 |