Mercurial > repos > dfornika > snippy

comparison snippy_core_wrapper.py @ 10:9d46ea31b273 draft

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planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
author dfornika
date Mon, 21 Jan 2019 19:03:51 -0500
parents caed59c13f82
children 502763099477
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9:caed59c13f82 10:9d46ea31b273
20 from shutil import copyfile 20 from shutil import copyfile
21 21
22 def main(): 22 def main():
23 parser = argparse.ArgumentParser() 23 parser = argparse.ArgumentParser()
24 parser.add_argument('-r', '--ref', help='Reference fasta', required=True) 24 parser.add_argument('-r', '--ref', help='Reference fasta', required=True)
25 parser.add_argument('-i', '--indirs' help='Comma-separated list of input datasets') 25 parser.add_argument('-i', '--indirs', help='Comma-separated list of input datasets')
26 args = parser.parse_args() 26 args = parser.parse_args()
27 27
28 snippy_core_command_line = ['snippy-core', '--ref', args.ref] 28 snippy_core_command_line = ['snippy-core', '--ref', args.ref]
29 29
30 for indir in args.indirs.split(','): 30 for indir in args.indirs.split(','):