view test-data/staramr/settings.txt @ 1:65a69de1e294 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834

command_line                  = /home/piemari/apps/conda/envs/amr/bin/staramr search --nprocs 4 --no-exclude-genes --pid-threshold 95 --percent-length-overlap-resfinder 90 --percent-length-overlap-pointfinder 90 --percent-length-overlap-plasmidfinder 90 --output-dir /storage/scratch/piemari/60579242/staramr/staramr_10_Enterococcus_faecalis_S17_L001 /storage/scratch/piemari/60579242/staramr/10_Enterococcus_faecalis_S17_L001.fasta
version                       = 0.9.1
start_time                    = 2023-02-13 14:26:11
end_time                      = 2023-02-13 14:26:13
total_minutes                 = 0.04
resfinder_db_dir              = /home/piemari/apps/conda/envs/amr/lib/python3.11/site-packages/staramr/databases/data/update/resfinder
resfinder_db_url              = https://bitbucket.org/genomicepidemiology/resfinder_db.git
resfinder_db_commit           = 23661dbb58797b302464855611223b7ba4a21f75
resfinder_db_date             = Fri, 02 Dec 2022 11:36
pointfinder_db_dir            = /home/piemari/apps/conda/envs/amr/lib/python3.11/site-packages/staramr/databases/data/update/pointfinder
pointfinder_db_url            = https://bitbucket.org/genomicepidemiology/pointfinder_db.git
pointfinder_db_commit         = a25ac32c7a7a904dff14ffbd17e3b3f7cd732954
pointfinder_db_date           = Fri, 28 Oct 2022 10:19
pointfinder_organisms_all     = campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, klebsiella, mycobacterium_tuberculosis, neisseria_gonorrhoeae, plasmodium_falciparum, salmonella, staphylococcus_aureus
pointfinder_organisms_valid   = campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, salmonella
plasmidfinder_db_dir          = /home/piemari/apps/conda/envs/amr/lib/python3.11/site-packages/staramr/databases/data/update/plasmidfinder
plasmidfinder_db_url          = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git
plasmidfinder_db_commit       = b1c9ddac0e618e07630a94452293d84f296a6de5
plasmidfinder_db_date         = Thu, 12 Jan 2023 12:51
mlst_version                  = 2.23.0
pointfinder_organism          = None
pointfinder_gene_drug_version = 072621.1
resfinder_gene_drug_version   = 072621