Description

Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD).

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

input_tsv{:bash}

:file

ARG annotation output

*.tsv

tool{:bash}

:string

ARG annotation tool used

argsoap|abricate|deeparg|resfinder|amrfinderplus

db{:bash}

:string

Database used for ARG annotation

sarg|ncbi|resfinder|deeparg|megares|argannot|resfinderfg

Output

name:type
description
pattern

tsv{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.tsv{:bash}

:file

Normalized argNorm output

*.tsv

versions_argnorm{:bash}

${task.process}{:bash}

:string

The name of the process

argnorm{:bash}

:string

The name of the tool

argnorm --version{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

argnorm{:bash}

:string

The name of the tool

argnorm --version{:bash}

:eval

The expression to obtain the version of the tool

Tools

argnorm
MIT

Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD).

argnorm.readthedocs.io/en/latest https://github.com/BigDataBiology/argNorm
included in
funcscan
maintainer
Github user Vedanth-Ramji
get in touch
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