Mercurial > repos > iuc > vsnp_add_zero_coverage
comparison vsnp_determine_ref_from_data.py @ 3:5b6d2f69bbc5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit a80e3713d10fafef22e964198d59251adf955812"
| author | iuc |
|---|---|
| date | Thu, 14 Jan 2021 09:08:44 +0000 |
| parents | 2e4b9161ce40 |
| children |
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| 2:2e4b9161ce40 | 3:5b6d2f69bbc5 |
|---|---|
| 195 | 195 |
| 196 | 196 |
| 197 if __name__ == '__main__': | 197 if __name__ == '__main__': |
| 198 parser = argparse.ArgumentParser() | 198 parser = argparse.ArgumentParser() |
| 199 | 199 |
| 200 parser.add_argument('--dnaprint_fields', action='append', dest='dnaprint_fields', nargs=2, required=False, default=None, help="List of dnaprints data table value, name and path fields") | 200 parser.add_argument('--dnaprint_fields', action='append', dest='dnaprint_fields', nargs=2, help="List of dnaprints data table value, name and path fields") |
| 201 parser.add_argument('--read1', action='store', dest='read1', required=True, default=None, help='Required: single read') | 201 parser.add_argument('--read1', action='store', dest='read1', help='Required: single read') |
| 202 parser.add_argument('--read2', action='store', dest='read2', required=False, default=None, help='Optional: paired read') | 202 parser.add_argument('--read2', action='store', dest='read2', required=False, default=None, help='Optional: paired read') |
| 203 parser.add_argument('--gzipped', action='store_true', dest='gzipped', default=False, help='Input files are gzipped') | 203 parser.add_argument('--gzipped', action='store_true', dest='gzipped', help='Input files are gzipped') |
| 204 parser.add_argument('--output_dbkey', action='store', dest='output_dbkey', required=True, default=None, help='Output reference file') | 204 parser.add_argument('--output_dbkey', action='store', dest='output_dbkey', help='Output reference file') |
| 205 parser.add_argument('--output_metrics', action='store', dest='output_metrics', required=True, default=None, help='Output metrics file') | 205 parser.add_argument('--output_metrics', action='store', dest='output_metrics', help='Output metrics file') |
| 206 | 206 |
| 207 args = parser.parse_args() | 207 args = parser.parse_args() |
| 208 | 208 |
| 209 fastq_list = [args.read1] | 209 fastq_list = [args.read1] |
| 210 if args.read2 is not None: | 210 if args.read2 is not None: |