Mercurial > repos > bgruening > bismark
comparison bismark_wrapper.py @ 10:7bffcb6fc81d draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 23685f742f0b5cd5de871c285d247d560485b11b
| author | bgruening |
|---|---|
| date | Tue, 26 Feb 2019 18:42:28 -0500 |
| parents | 9bfe38410155 |
| children | a4504327c890 |
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| 9:1a88b0f2669f | 10:7bffcb6fc81d |
|---|---|
| 66 help='The single-end reads file in Sanger FASTQ or FASTA format.') | 66 help='The single-end reads file in Sanger FASTQ or FASTA format.') |
| 67 | 67 |
| 68 parser.add_argument('--fastq', action='store_true', help='Query filetype is in FASTQ format') | 68 parser.add_argument('--fastq', action='store_true', help='Query filetype is in FASTQ format') |
| 69 parser.add_argument('--fasta', action='store_true', help='Query filetype is in FASTA format') | 69 parser.add_argument('--fasta', action='store_true', help='Query filetype is in FASTA format') |
| 70 parser.add_argument('--phred64-quals', dest='phred64', action="store_true") | 70 parser.add_argument('--phred64-quals', dest='phred64', action="store_true") |
| 71 parser.add_argument('--non-directional', dest='non_directional', action="store_true") | |
| 71 | 72 |
| 72 parser.add_argument('--skip-reads', dest='skip_reads', type=int) | 73 parser.add_argument('--skip-reads', dest='skip_reads', type=int) |
| 73 parser.add_argument('--qupto', type=int) | 74 parser.add_argument('--qupto', type=int) |
| 74 | 75 |
| 75 # paired end options | 76 # paired end options |
| 182 cmd.extend(['--skip', str(args.skip_reads)]) | 183 cmd.extend(['--skip', str(args.skip_reads)]) |
| 183 if args.qupto: | 184 if args.qupto: |
| 184 cmd.extend(['--upto', 'args.qupto']) | 185 cmd.extend(['--upto', 'args.qupto']) |
| 185 if args.phred64: | 186 if args.phred64: |
| 186 cmd.append('--phred64-quals') | 187 cmd.append('--phred64-quals') |
| 188 if args.non_directional: | |
| 189 cmd.append('--non-directional') | |
| 187 if args.suppress_header: | 190 if args.suppress_header: |
| 188 cmd.append('--sam-no-hd') | 191 cmd.append('--sam-no-hd') |
| 189 if args.output_unmapped_reads or (args.output_unmapped_reads_l and args.output_unmapped_reads_r): | 192 if args.output_unmapped_reads or (args.output_unmapped_reads_l and args.output_unmapped_reads_r): |
| 190 cmd.append('--un') | 193 cmd.append('--un') |
| 191 if args.output_suppressed_reads or (args.output_suppressed_reads_l and args.output_suppressed_reads_r): | 194 if args.output_suppressed_reads or (args.output_suppressed_reads_l and args.output_suppressed_reads_r): |