Mercurial > repos > bgruening > bismark
comparison bismark_wrapper.py @ 16:a4504327c890 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit ce4520063ab4d016dd5c5680c0f03eae849b150c"
author | bgruening |
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date | Wed, 21 Aug 2019 12:59:48 -0400 |
parents | 7bffcb6fc81d |
children | aa9bf0f29a9f |
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15:0b656f8c5637 | 16:a4504327c890 |
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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 parser.add_argument('--non-directional', dest='non_directional', action="store_true") |
72 | 72 |
73 parser.add_argument('--skip-reads', dest='skip_reads', type=int) | 73 parser.add_argument('--skip-reads', dest='skip_reads', type=int) |
74 parser.add_argument('--score-min', dest='score_min', type=str) | |
74 parser.add_argument('--qupto', type=int) | 75 parser.add_argument('--qupto', type=int) |
75 | 76 |
76 # paired end options | 77 # paired end options |
77 parser.add_argument('-I', '--minins', dest='min_insert') | 78 parser.add_argument('-I', '--minins', dest='min_insert') |
78 parser.add_argument('-X', '--maxins', dest='max_insert') | 79 parser.add_argument('-X', '--maxins', dest='max_insert') |
86 parser.add_argument('--seed-extention-attempts', dest='seed_extention_attempts', type=int) | 87 parser.add_argument('--seed-extention-attempts', dest='seed_extention_attempts', type=int) |
87 # default 0 | 88 # default 0 |
88 parser.add_argument('--seed-mismatches', dest='seed_mismatches', type=int) | 89 parser.add_argument('--seed-mismatches', dest='seed_mismatches', type=int) |
89 # default 2 | 90 # default 2 |
90 parser.add_argument('--max-reseed', dest='max_reseed', type=int) | 91 parser.add_argument('--max-reseed', dest='max_reseed', type=int) |
91 """ | 92 |
92 # default 70 | |
93 parser.add_argument( '--maqerr', dest='maqerr', type=int ) | |
94 """ | |
95 | 93 |
96 """ | 94 """ |
97 The number of megabytes of memory a given thread is given to store path | 95 The number of megabytes of memory a given thread is given to store path |
98 descriptors in --best mode. Best-first search must keep track of many paths | 96 descriptors in --best mode. Best-first search must keep track of many paths |
99 at once to ensure it is always extending the path with the lowest cumulative | 97 at once to ensure it is always extending the path with the lowest cumulative |
179 cmd.append('--no-discordant') | 177 cmd.append('--no-discordant') |
180 if args.no_mixed: | 178 if args.no_mixed: |
181 cmd.append('--no-mixed') | 179 cmd.append('--no-mixed') |
182 if args.skip_reads: | 180 if args.skip_reads: |
183 cmd.extend(['--skip', str(args.skip_reads)]) | 181 cmd.extend(['--skip', str(args.skip_reads)]) |
182 if args.score_min: | |
183 cmd.extend(['--score_min', str(args.score_min)]) | |
184 if args.qupto: | 184 if args.qupto: |
185 cmd.extend(['--upto', 'args.qupto']) | 185 cmd.extend(['--upto', 'args.qupto']) |
186 if args.phred64: | 186 if args.phred64: |
187 cmd.append('--phred64-quals') | 187 cmd.append('--phred64-quals') |
188 if args.non_directional: | 188 if args.non_directional: |