# HG changeset patch
# User iss
# Date 1647938350 0
# Node ID 444b0421bbdc8581a90a7bcd5b781a56a3a3d6d8
# Parent  c6bab5103a14620d41f5d24498e09bbbde107a61
"planemo upload commit c8533b93fb2816db37887244489cbd6e919fc155"

diff -r c6bab5103a14 -r 444b0421bbdc EURL_VTEC_WGS_PT.py
--- 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)
diff -r c6bab5103a14 -r 444b0421bbdc README.md
--- a/README.md	Mon Mar 21 15:23:09 2022 +0000
+++ b/README.md	Tue Mar 22 08:39:10 2022 +0000
@@ -1,5 +1,5 @@
 # eurl_vtec_wgs_pt-galaxy
- This tool performs various Escherichia coli typing tools and is implemented as a Galaxy (https://galaxyproject.org/) workflow
+ This workflow performs various Escherichia coli typing tools and is implemented as a Galaxy (https://galaxyproject.org/) workflow
 
     Raw data quality check (FASTQC, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
     Trimming (Trimmomatic, DOI:10.1093/bioinformatics/btu170)
@@ -9,4 +9,4 @@
     Shigatoxintyping (blastn, DOI:10.1186/1471-2105-10-421, of a consensus sequence against the shiga toxin subtype database from the Statens Serum Institut SSI and Technical University of Denmark DTU, DOI:10.1128/JCM.00008-15)
     AMR typing (Abricate, Seemann T, Github https://github.com/tseemann/abricate; ResFinder database DOI:10.1093/jac/dks261)
 
-After installation the BASE_URL parameter in the EURL_VTEC_WGS_PT.py file (line 20) will have to be modified to the url of your Galaxy instance in order to correctly visualise the FastQC results.  
+The value of `galaxy_infrastructure_url` in the galaxy.yml file has to be set to the url of your Galaxy instance in order to correctly visualise the FastQC and AMR results.  
diff -r c6bab5103a14 -r 444b0421bbdc eurl_vtec_wgs_pt.xml
--- a/eurl_vtec_wgs_pt.xml	Mon Mar 21 15:23:09 2022 +0000
+++ b/eurl_vtec_wgs_pt.xml	Tue Mar 22 08:39:10 2022 +0000
@@ -26,7 +26,8 @@
     <command>
 <![CDATA[
       python
-      $__tool_directory__/EURL_VTEC_WGS_PT.py --log $logfile --output $report_out --contigs $contigs --quast $quast --mlstsevenloci $mlstsevenloci
+      $__tool_directory__/EURL_VTEC_WGS_PT.py --base_url $__app__.config.galaxy_infrastructure_url --log $logfile --output $report_out
+	  --contigs $contigs --quast $quast --mlstsevenloci $mlstsevenloci
       #if str( $library.type ) == "single":
           -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}' 
           --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path}