Mercurial > repos > iss > eurl_vtec_wgs_pt
diff README.md @ 1:444b0421bbdc draft
"planemo upload commit c8533b93fb2816db37887244489cbd6e919fc155"
| author | iss |
|---|---|
| date | Tue, 22 Mar 2022 08:39:10 +0000 |
| parents | c6bab5103a14 |
| children |
line wrap: on
line diff
--- 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.