Mercurial > repos > mheinzl > variant_analyzer2
diff 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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--- a/read2mut.py Mon Feb 15 21:53:24 2021 +0000 +++ b/read2mut.py Tue Feb 16 07:08:25 2021 +0000 @@ -46,7 +46,11 @@ parser.add_argument('--sscsJson', help='JSON file with SSCS counts collected by mut2sscs.py.') parser.add_argument('--outputFile', - help='Output xlsx file of mutation details.') + help='Output xlsx file with summary of mutations.') + parser.add_argument('--outputFile2', + help='Output xlsx file with allele frequencies of mutations.') + parser.add_argument('--outputFile3', + help='Output xlsx file with examples of the tier classification.') parser.add_argument('--thresh', type=int, default=0, help='Integer threshold for displaying mutations. Only mutations occuring less than thresh times are displayed. Default of 0 displays all.') parser.add_argument('--phred', type=int, default=20, @@ -72,6 +76,8 @@ json_file = args.inputJson sscs_json = args.sscsJson outfile = args.outputFile + outfile2 = args.outputFile2 + outfile3 = args.outputFile3 thresh = args.thresh phred_score = args.phred trim = args.trim