Mercurial > repos > iss > eurl_vtec_wgs_pt

comparison EURL_VTEC_WGS_PT.py @ 1:444b0421bbdc draft

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"planemo upload commit c8533b93fb2816db37887244489cbd6e919fc155"
author iss
date Tue, 22 Mar 2022 08:39:10 +0000
parents c6bab5103a14
children 32b5625795ea
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0:c6bab5103a14 1:444b0421bbdc
15 import subprocess 15 import subprocess
16 import HTML 16 import HTML
17 import datetime 17 import datetime
18 import fileinput 18 import fileinput
19 19
20 BASE_URL = 'https://aries.iss.it'
21 TOOL_DIR = os.path.dirname(os.path.abspath(__file__)) 20 TOOL_DIR = os.path.dirname(os.path.abspath(__file__))
22 21
23 def insertFile(filename, report): 22 def insertFile(filename, report):
24 with open(filename) as html_in: 23 with open(filename) as html_in:
25 for line in html_in: 24 for line in html_in:
62 parser.add_argument('--html2_id', dest='html2_id', help='html FASTQC file id') 61 parser.add_argument('--html2_id', dest='html2_id', help='html FASTQC file id')
63 parser.add_argument('--html2_path', dest='html2_path', help='html FASTQC file path') 62 parser.add_argument('--html2_path', dest='html2_path', help='html FASTQC file path')
64 parser.add_argument('--text2', dest='text2', help='text FASTQC file') 63 parser.add_argument('--text2', dest='text2', help='text FASTQC file')
65 parser.add_argument('--contigs', dest='contigs', help='Assembly contigs') 64 parser.add_argument('--contigs', dest='contigs', help='Assembly contigs')
66 parser.add_argument('--quast', dest='quast', help='Quast report') 65 parser.add_argument('--quast', dest='quast', help='Quast report')
66 parser.add_argument('--base_url', dest='base_url', help='base_url')
67 parser.add_argument('--log', dest='logfile', help='log file') 67 parser.add_argument('--log', dest='logfile', help='log file')
68 parser.add_argument('--virulotyper', dest='virulotyper', help='Virulotyping Mapping reads') 68 parser.add_argument('--virulotyper', dest='virulotyper', help='Virulotyping Mapping reads')
69 parser.add_argument('--virulotyper_id', dest='virulotyper_id', help='Virulotyping Mapping reads id') 69 parser.add_argument('--virulotyper_id', dest='virulotyper_id', help='Virulotyping Mapping reads id')
70 parser.add_argument('--stx', dest='stx', help='Shiga toxin') 70 parser.add_argument('--stx', dest='stx', help='Shiga toxin')
71 parser.add_argument('--mlstsevenloci', dest='mlstsevenloci', help='Multi Locus Alleles table') 71 parser.add_argument('--mlstsevenloci', dest='mlstsevenloci', help='Multi Locus Alleles table')
74 parser.add_argument('--antigen_O', dest='antigen_O', help='Antigen for O') 74 parser.add_argument('--antigen_O', dest='antigen_O', help='Antigen for O')
75 parser.add_argument('--antigen_H', dest='antigen_H', help='Antigen for H') 75 parser.add_argument('--antigen_H', dest='antigen_H', help='Antigen for H')
76 parser.add_argument('--output', dest='output', help='output report html file') 76 parser.add_argument('--output', dest='output', help='output report html file')
77 args = parser.parse_args() 77 args = parser.parse_args()
78 78
79 BASE_URL = args.base_url
79 log = open(args.logfile, 'w') 80 log = open(args.logfile, 'w')
80 log.write("EURL VTEC WGS PT v3.2\n\nTool versions\n=============\n") 81 log.write("EURL VTEC WGS PT v4.0\n\nTool versions\n=============\n")
81 os.system("ln -s $(readlink -e $(which trimmomatic)).jar trimmomatic.jar") 82 os.system("ln -s $(readlink -e $(which trimmomatic)).jar trimmomatic.jar")
82 # FASTQC 83 # FASTQC
83 subprocess.call("python " + TOOL_DIR + "/scripts/rgFastQC.py -i " + args.input1 + " -d " + args.html1_path + " -o " + args.html1 + " -t " + args.text1 + " -f " + args.input1_ext + " -j " + args.input1_name + " -e " + "fastqc", shell=True) 84 subprocess.call("python " + TOOL_DIR + "/scripts/rgFastQC.py -i " + args.input1 + " -d " + args.html1_path + " -o " + args.html1 + " -t " + args.text1 + " -f " + args.input1_ext + " -j " + args.input1_name + " -e " + "fastqc", shell=True)
84 log.write(os.popen("fastqc -v").read()) 85 log.write(os.popen("fastqc -v").read())
85 if args.input2: 86 if args.input2: