Mercurial > repos > dfornika > snippy

diff snippy_core_wrapper.py @ 9:caed59c13f82 draft
planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
author: dfornika
date: Mon, 21 Jan 2019 18:35:52 -0500
parents: c441153cb4c2
children: 9d46ea31b273
--- a/snippy_core_wrapper.py	Mon Jan 21 18:26:12 2019 -0500
+++ b/snippy_core_wrapper.py	Mon Jan 21 18:35:52 2019 -0500
@@ -22,12 +22,12 @@
 def main():
     parser = argparse.ArgumentParser()
     parser.add_argument('-r', '--ref', help='Reference fasta', required=True)
-    parser.add_argument('-i', '--indirs')
+    parser.add_argument('-i', '--indirs' help='Comma-separated list of input datasets')
     args = parser.parse_args()
 
     snippy_core_command_line = ['snippy-core', '--ref', args.ref]
 
-    for indir in args.indirs.split():
+    for indir in args.indirs.split(','):
         base_name = os.path.basename(indir)
         sys.stderr.write(indir + '\n')
         copyfile(indir, base_name)