Mercurial > repos > iss > eurl_vtec_wgs_pt
diff EURL_VTEC_WGS_PT.py @ 1:444b0421bbdc draft
"planemo upload commit c8533b93fb2816db37887244489cbd6e919fc155"
| author | iss |
|---|---|
| date | Tue, 22 Mar 2022 08:39:10 +0000 |
| parents | c6bab5103a14 |
| children | 32b5625795ea |
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--- a/EURL_VTEC_WGS_PT.py Mon Mar 21 15:23:09 2022 +0000 +++ b/EURL_VTEC_WGS_PT.py Tue Mar 22 08:39:10 2022 +0000 @@ -17,7 +17,6 @@ import datetime import fileinput -BASE_URL = 'https://aries.iss.it' TOOL_DIR = os.path.dirname(os.path.abspath(__file__)) def insertFile(filename, report): @@ -64,6 +63,7 @@ parser.add_argument('--text2', dest='text2', help='text FASTQC file') parser.add_argument('--contigs', dest='contigs', help='Assembly contigs') parser.add_argument('--quast', dest='quast', help='Quast report') + parser.add_argument('--base_url', dest='base_url', help='base_url') parser.add_argument('--log', dest='logfile', help='log file') parser.add_argument('--virulotyper', dest='virulotyper', help='Virulotyping Mapping reads') parser.add_argument('--virulotyper_id', dest='virulotyper_id', help='Virulotyping Mapping reads id') @@ -76,8 +76,9 @@ parser.add_argument('--output', dest='output', help='output report html file') args = parser.parse_args() + BASE_URL = args.base_url log = open(args.logfile, 'w') - log.write("EURL VTEC WGS PT v3.2\n\nTool versions\n=============\n") + log.write("EURL VTEC WGS PT v4.0\n\nTool versions\n=============\n") os.system("ln -s $(readlink -e $(which trimmomatic)).jar trimmomatic.jar") # FASTQC 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)