Mercurial > repos > bgruening > bismark
diff 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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--- a/bismark_wrapper.py Fri Feb 22 14:15:46 2019 -0500 +++ b/bismark_wrapper.py Tue Feb 26 18:42:28 2019 -0500 @@ -68,6 +68,7 @@ parser.add_argument('--fastq', action='store_true', help='Query filetype is in FASTQ format') parser.add_argument('--fasta', action='store_true', help='Query filetype is in FASTA format') parser.add_argument('--phred64-quals', dest='phred64', action="store_true") + parser.add_argument('--non-directional', dest='non_directional', action="store_true") parser.add_argument('--skip-reads', dest='skip_reads', type=int) parser.add_argument('--qupto', type=int) @@ -184,6 +185,8 @@ cmd.extend(['--upto', 'args.qupto']) if args.phred64: cmd.append('--phred64-quals') + if args.non_directional: + cmd.append('--non-directional') if args.suppress_header: cmd.append('--sam-no-hd') if args.output_unmapped_reads or (args.output_unmapped_reads_l and args.output_unmapped_reads_r):