From e63ad79c6a0dd80cba3a6d88d00f08bbc1f55c53 Mon Sep 17 00:00:00 2001
From: Martin RETHORET-PASTY <martin.rethoret-pasty@pasteur.fr>
Date: Mon, 16 Oct 2023 11:56:51 +0200
Subject: [PATCH] Updating Readme
---
README.md | 10 +++++++---
1 file changed, 7 insertions(+), 3 deletions(-)
diff --git a/README.md b/README.md
index 500a297..3eaec80 100755
--- a/README.md
+++ b/README.md
@@ -56,17 +56,21 @@ usage: __main__.py -a ASSEMBLIES [ASSEMBLIES ...] [-u] [-t] [-res_vir] [-plus] [
diphtOscan: a tool for characterising virulence and resistance in Corynebacterium
+Updating option:
+ -u, --update Update database MLST, Tox Allele & AMR (default: no).The database update can be executed on its own without the -a option.
+
Required arguments:
-a ASSEMBLIES [ASSEMBLIES ...], --assemblies ASSEMBLIES [ASSEMBLIES ...]
- FASTA file(s) for assemblies
+ FASTA file(s) for assemblies.
Screening options:
- -u, --update Update database MLST et AMR (default: no)
- -t, --taxonomy Turn on species Corynebacterium diphtheriae species complex (CdSC) and MLST sequence type
+ -st, --mlst Turn on species Corynebacterium diphtheriae species complex (CdSC) and MLST sequence type
(default: no)
+ -t, --tox Turn on tox allele (default: no)
-res_vir, --resistance_virulence
Turn on resistance and virulence genes screening (default: no resistance and virulence gene
screening)
+
-plus, --extend_genotyping
Turn on all virulence genes screening (default: no all virulence gene screening)
-integron, --integron
--
GitLab