Mercurial > repos > jjjjia > cpo_prediction

comparison cpo_galaxy_prediction.py @ 21:1543496b2db4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author jjjjia
date Tue, 28 Aug 2018 19:23:31 -0400
parents 596bf8a792de
children e03c8f2d2629
comparison
equal deleted inserted replaced
20:47502be81f6a 21:1543496b2db4
40 parser.add_option("-a", "--abricate", dest="abricate", type="string", help="absolute path to abricate results") 40 parser.add_option("-a", "--abricate", dest="abricate", type="string", help="absolute path to abricate results")
41 parser.add_option("-r", "--rgi", dest="rgi", type="string", help="absolute path to rgi results") 41 parser.add_option("-r", "--rgi", dest="rgi", type="string", help="absolute path to rgi results")
42 parser.add_option("-e", "--expected", dest="expectedSpecies", default="NA/NA/NA", type="string", help="expected species of the isolate") 42 parser.add_option("-e", "--expected", dest="expectedSpecies", default="NA/NA/NA", type="string", help="expected species of the isolate")
43 parser.add_option("-s", "--mlst-scheme", dest="mlstScheme", default= "./scheme_species_map.tab", type="string", help="absolute file path to mlst scheme") 43 parser.add_option("-s", "--mlst-scheme", dest="mlstScheme", default= "./scheme_species_map.tab", type="string", help="absolute file path to mlst scheme")
44 parser.add_option("-p", "--plasmidfinder", dest="plasmidfinder", type="string", help="absolute file path to plasmidfinder ") 44 parser.add_option("-p", "--plasmidfinder", dest="plasmidfinder", type="string", help="absolute file path to plasmidfinder ")
45 parser.add_options("-d", "--mash", dest="mash", type="string", help="absolute file path to mash plasmiddb result") 45 parser.add_option("-d", "--mash", dest="mash", type="string", help="absolute file path to mash plasmiddb result")
46 46
47 #parallelization, useless, these are hard coded to 8cores/64G RAM 47 #parallelization, useless, these are hard coded to 8cores/64G RAM
48 #parser.add_option("-t", "--threads", dest="threads", default=8, type="int", help="number of cpu to use") 48 #parser.add_option("-t", "--threads", dest="threads", default=8, type="int", help="number of cpu to use")
49 #parser.add_option("-p", "--memory", dest="memory", default=64, type="int", help="memory to use in GB") 49 #parser.add_option("-p", "--memory", dest="memory", default=64, type="int", help="memory to use in GB")
50 50