Mercurial > repos > iss > eurl_vtec_wgs_pt
changeset 1:444b0421bbdc draft
"planemo upload commit c8533b93fb2816db37887244489cbd6e919fc155"
| author | iss |
|---|---|
| date | Tue, 22 Mar 2022 08:39:10 +0000 |
| parents | c6bab5103a14 |
| children | 65378117a8c0 |
| files | EURL_VTEC_WGS_PT.py README.md eurl_vtec_wgs_pt.xml |
| diffstat | 3 files changed, 7 insertions(+), 5 deletions(-) [+] |
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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)
--- 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.
--- 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}