Mercurial > repos > rakesh4osdd > asist
changeset 1:9c7d056cac30 draft
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 2d3fa913c9fa9db73f4aa40799749f2247abaa80-dirty"
| author | rakesh4osdd |
|---|---|
| date | Mon, 28 Jun 2021 14:39:22 +0000 |
| parents | c1a77856070c |
| children | 62afd73a0987 |
| files | clsi.csv input.csv test-data/input.csv tool_shed.sh |
| diffstat | 3 files changed, 2 insertions(+), 55 deletions(-) [+] |
line wrap: on
line diff
--- a/clsi.csv Sat Jun 26 07:27:53 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -Antibiotics,Susceptible,Resistant,Intermediate -Amikacin,≤ 16,≥ 64,32 -Tobramycin,≤ 4,≥ 16,8 -Gentamicin,≤ 4,≥ 16,8 -Netilmicin,≤ 8,≥ 32,16 -Imipenem,≤ 2,≥ 8,4 -Meropenem,≤ 2,≥ 8,4 -Doripenem,≤ 2,≥ 8,4 -Ciprofloxacin,≤ 1,≥ 4,2 -Levofloxacin,≤ 2,≥ 8,4 -Piperacillin/ tazobactam,≤ 16/4,≥ 128/4,32/4-64/4 -Ticarcillin/ clavulanic acid,≤ 16/2,≥ 128/2,32/2-64/2 -Cefotaxime,≤ 8,≥ 64,16-32 -Ceftriaxone,≤ 8,≥ 64,16-32 -Ceftazidime,≤ 8,≥ 32,16 -Cefepime,≤ 8,≥ 32,16 -Trimethoprim/ sulfamethoxazole,≤ 2/38,≥ 4/76,- -Ampicillin/ sulbactam,≤ 8/4,≥ 32/16,16/8 -Colistin,-,≥ 4,≤ 2 -Polymyxin B,-,≥ 4,≤ 2 -Tetracycline,≤ 4,≥ 16,8 -Doxycycline,≤ 4,≥ 16,8 -Minocycline,≤ 4,≥ 16,8 \ No newline at end of file
--- a/input.csv Sat Jun 26 07:27:53 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ -id,genome Ids,Strain name,Antibiotics,Resistance_profile,sign,MIC,unit -470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,0.1,mg/L -470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,1,mg/L -470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,2,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin,resistant,>=,0,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin/sulbactam,susceptible,<=,mg/L,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,piperacillin/tazobactam,susceptible,<=,0,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefazolin,resistant,>=,64,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Ceftriaxone,susceptible,==,16,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefepime,susceptible,==,8,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Meropenem,susceptible,<=,0.25,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Imipenem,susceptible,<=,1,mg/L -470,CP001172.2,Acinetobacter baumannii AB307-0294,Tigecycline,susceptible,<=,0.5,mg/L -470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ceftazidime,Resistant,NA,>128,mg/L -470,CP008706.1,Acinetobacter baumannii AB5075-UW,Cefepime,Resistant,NA,>256,mg/L -470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ciprofloxacin,Resistant,NA,>32,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,colistin ,Susceptible,NA,,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,Ampicillin/sulbactam,Resistant,NA,>=0.3 mg/L,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,ticarcillin/clavulanic acid,Resistant,NA,>=128/2,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,piperacillin/tazobactam ,Resistant,NA,NA,mg/L -470,CP017152.1,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L -470,CP015483.1,Acinetobacter baumannii ORAB01,piperacillin/tazobactam,Resistant,NA,>64/4,mg/L -470,470.7601,Acinetobacter baumannii strain MRSN7100,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L -470,470.7651,Acinetobacter baumannii strain MRSN7168,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L -470,470.7764,Acinetobacter baumannii strain MRSN7336,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L -470,470.8071,Acinetobacter baumannii strain MRSN7834,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L -470,470.7405,Acinetobacter baumannii strain FDA-CDC-AR_0305,polymyxin B,Susceptible,==,1,mg/L -470,470.7406,Acinetobacter baumannii strain FDA-CDC-AR_0306,polymyxin B,Susceptible,==,1,mg/L -470,470.7407,Acinetobacter baumannii strain FDA-CDC-AR_0307,polymyxin B,Resistant,==,8,mg/L -470,470.7408,Acinetobacter baumannii strain FDA-CDC-AR_0308,polymyxin B,Resistant,==,4,mg/L
--- a/tool_shed.sh Sat Jun 26 07:27:53 2021 +0000 +++ b/tool_shed.sh Mon Jun 28 14:39:22 2021 +0000 @@ -1,4 +1,5 @@ #!/bin/bash # After reviewing .shed.yml, this configuration file and relevant shed artifacts can be quickly linted using the following command. planemo shed_lint --tools -planemo shed_create --shed_target toolshed +#planemo shed_create --shed_target toolshed +planemo shed_update --check_diff --shed_target toolshed