Mercurial > repos > bgruening > bismark

comparison bismark_methylation_extractor.py @ 20:ff6ee551b153 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 2d8f9bfd501f1cd82b5cf0429c1b02b3784392ab"
author bgruening
date Fri, 04 Oct 2019 11:33:27 -0400
parents 9bfe38410155
children 120b7b35e442
comparison
equal deleted inserted replaced
19:359f8b60d316 20:ff6ee551b153
95 output_dir = tempfile.mkdtemp() 95 output_dir = tempfile.mkdtemp()
96 cmd = ['bismark_methylation_extractor', '--no_header', '-o', output_dir] 96 cmd = ['bismark_methylation_extractor', '--no_header', '-o', output_dir]
97 # Set up all options 97 # Set up all options
98 if args.multicore > 3: 98 if args.multicore > 3:
99 # divide multicore by 3 here since bismark will spawn ~3 jobs. 99 # divide multicore by 3 here since bismark will spawn ~3 jobs.
100 cmd.extend(['--multicore', str(math.ceil(args.multicore / 3))]) 100 cmd.extend(['--multicore', str(int(math.floor(args.multicore / 3)))])
101 if args.single_end: 101 if args.single_end:
102 cmd.append('--single-end') 102 cmd.append('--single-end')
103 else: 103 else:
104 cmd.append('--paired-end') 104 cmd.append('--paired-end')
105 if args.no_overlap: 105 if args.no_overlap: