Mercurial > repos > jdv > albacore

comparison albacore_1D.py @ 8:3dfde840119e draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 8bb4eaadc31e6b986bee59392559a825c782447c-dirty
author jdv
date Mon, 18 Jun 2018 12:20:28 -0400
parents ce1fa05ffb6c
children
comparison
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7:ce1fa05ffb6c 8:3dfde840119e
9 import numpy as np 9 import numpy as np
10 from distutils.util import strtobool 10 from distutils.util import strtobool
11 from tempfile import mkdtemp 11 from tempfile import mkdtemp
12 12
13 def main(): 13 def main():
14 tar_file = sys.argv[1] 14 tar_file = sys.argv[1]
15 out_file = sys.argv[2] 15 out_file = sys.argv[2]
16 out_fmt = sys.argv[3] 16 out_fmt = sys.argv[3]
17 demux = strtobool( sys.argv[4] ) 17 demux = strtobool( sys.argv[4] )
18 threads = sys.argv[5] 18 disable_filt = strtobool( sys.argv[5] )
19 threads = sys.argv[6]
19 20
20 tempdir = mkdtemp() 21 tempdir = mkdtemp()
21 22
22 (flowcell, kit) = parse_meta(tar_file, tempdir) 23 (flowcell, kit) = parse_meta(tar_file, tempdir)
23 24
30 "--kit", kit, 31 "--kit", kit,
31 "--recursive", 32 "--recursive",
32 "--files_per_batch_folder", "0", 33 "--files_per_batch_folder", "0",
33 "--output_format", out_fmt, 34 "--output_format", out_fmt,
34 "--reads_per_fastq_batch", "999999999" ] + 35 "--reads_per_fastq_batch", "999999999" ] +
35 ["--barcoding"] * demux ) 36 ["--barcoding"] * demux +
37 ["--disable_filtering"] * disable_filt )
36 38
37 out_path = "out_dir/workspace" 39 out_path = "out_dir/workspace"
38 pass_path = os.path.join( out_path, "pass" ) 40 pass_path = os.path.join( out_path, "pass" )
39 if os.path.exists( pass_path ): 41 if os.path.exists( pass_path ):
40 out_path = pass_path 42 out_path = pass_path