Mercurial > repos > mheinzl > variant_analyzer2
comparison read2mut.py @ 12:7a418148319d draft
planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
| author | mheinzl |
|---|---|
| date | Tue, 16 Feb 2021 07:08:25 +0000 |
| parents | 84a1a3f70407 |
| children | 02bf6425fc25 |
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| 11:84a1a3f70407 | 12:7a418148319d |
|---|---|
| 44 parser.add_argument('--inputJson', | 44 parser.add_argument('--inputJson', |
| 45 help='JSON file with data collected by mut2read.py.') | 45 help='JSON file with data collected by mut2read.py.') |
| 46 parser.add_argument('--sscsJson', | 46 parser.add_argument('--sscsJson', |
| 47 help='JSON file with SSCS counts collected by mut2sscs.py.') | 47 help='JSON file with SSCS counts collected by mut2sscs.py.') |
| 48 parser.add_argument('--outputFile', | 48 parser.add_argument('--outputFile', |
| 49 help='Output xlsx file of mutation details.') | 49 help='Output xlsx file with summary of mutations.') |
| 50 parser.add_argument('--outputFile2', | |
| 51 help='Output xlsx file with allele frequencies of mutations.') | |
| 52 parser.add_argument('--outputFile3', | |
| 53 help='Output xlsx file with examples of the tier classification.') | |
| 50 parser.add_argument('--thresh', type=int, default=0, | 54 parser.add_argument('--thresh', type=int, default=0, |
| 51 help='Integer threshold for displaying mutations. Only mutations occuring less than thresh times are displayed. Default of 0 displays all.') | 55 help='Integer threshold for displaying mutations. Only mutations occuring less than thresh times are displayed. Default of 0 displays all.') |
| 52 parser.add_argument('--phred', type=int, default=20, | 56 parser.add_argument('--phred', type=int, default=20, |
| 53 help='Integer threshold for Phred score. Only reads higher than this threshold are considered. Default 20.') | 57 help='Integer threshold for Phred score. Only reads higher than this threshold are considered. Default 20.') |
| 54 parser.add_argument('--trim', type=int, default=10, | 58 parser.add_argument('--trim', type=int, default=10, |
| 70 file1 = args.mutFile | 74 file1 = args.mutFile |
| 71 file2 = args.bamFile | 75 file2 = args.bamFile |
| 72 json_file = args.inputJson | 76 json_file = args.inputJson |
| 73 sscs_json = args.sscsJson | 77 sscs_json = args.sscsJson |
| 74 outfile = args.outputFile | 78 outfile = args.outputFile |
| 79 outfile2 = args.outputFile2 | |
| 80 outfile3 = args.outputFile3 | |
| 75 thresh = args.thresh | 81 thresh = args.thresh |
| 76 phred_score = args.phred | 82 phred_score = args.phred |
| 77 trim = args.trim | 83 trim = args.trim |
| 78 chimera_correction = args.chimera_correction | 84 chimera_correction = args.chimera_correction |
| 79 | 85 |