Description

Tool to convert and summarize DeepARG outputs using the hAMRonization specification

Input

name:type
description
pattern

meta

:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

report

:file

Output .mapping.ARG file from DeepARG

*.mapping.ARG

format

:string

Type of report file to be produced

tsv|json

software_version

:string

Version of DeepARG used

[0-9].[0-9].[0-9]

reference_db_version

:integer

Database version of DeepARG used

[0-9]

Output

name:type
description
pattern

json

meta

:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

*.json

:file

hAMRonised report in JSON format

*.json

tsv

meta

:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

*.tsv

:file

hAMRonised report in TSV format

*.json

versions_hamronization

${task.process}

:string

The name of the process

hamronization

:string

The name of the tool

hamronize --version 2>&1 | sed 's/hamronize //'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

hamronization

:string

The name of the tool

hamronize --version 2>&1 | sed 's/hamronize //'

:eval

The expression to obtain the version of the tool

Tools

hamronization
GNU Lesser General Public v3 (LGPL v3)

Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification

github.com/pha4ge/hAMRonization https://github.com/pha4ge/hAMRonization
included in
funcscan
maintainer
Github user jfy133
get in touch
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