modules/ampir

A fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs.

ampirampantimicrobial peptide prediction

https://github.com/nf-core/modules/[...]/modules/nf-core/ampir

Description

A fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs.

Input

name:type

description

pattern

`meta`
`:map`

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

`faa`
`:file`

FASTA file containing amino acid sequences

*.{faa,fasta}

`model`
`:string`

Built-in model for AMP prediction

{precursor,mature}

`min_length`
`:integer`

Minimum protein length for which predictions will be generated

[0-9]+

`min_probability`
`:float`

Cut-off for AMP prediction

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

Output

name:type

description

pattern

`amps_faa`

`meta`
`:map`

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

`*.faa`
`:file`

File containing AMP predictions in amino acid FASTA format

*.{faa}

`amps_tsv`

`meta`
`:map`

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

`*.tsv`
`:file`

File containing AMP predictions in TSV format

*.tsv

`versions_ampir`

`${task.process}`
`:string`

The name of the process

`ampir`
`:string`

The name of the tool

`Rscript -e "library(ampir); cat(paste((unlist(packageVersion('ampir'))), collapse = '.'))"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`ampir`
`:string`

The name of the tool

`Rscript -e "library(ampir); cat(paste((unlist(packageVersion('ampir'))), collapse = '.'))"`
`:eval`

The expression to obtain the version of the tool

Tools

ampir
GPL v2

A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale.

github.com/Legana/ampir cran.r-project.org/web/packages/ampir https://github.com/Legana/ampir 10.1093/bioinformatics/btaa653

modules/ampir

Description

Input

`meta`
`:map`

`faa`
`:file`

`model`
`:string`

`min_length`
`:integer`

`min_probability`
`:float`

Output

`amps_faa`

`meta`
`:map`

`*.faa`
`:file`

`amps_tsv`

`meta`
`:map`

`*.tsv`
`:file`

`versions_ampir`

`${task.process}`
`:string`

`ampir`
`:string`

`Rscript -e "library(ampir); cat(paste((unlist(packageVersion('ampir'))), collapse = '.'))"`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`ampir`
`:string`

`Rscript -e "library(ampir); cat(paste((unlist(packageVersion('ampir'))), collapse = '.'))"`
`:eval`

Tools

ampir
GPL v2

included in

maintainer

get in touch

modules/ampir

Description

Input

meta:map

faa:file

model:string

min_length:integer

min_probability:float

Output

amps_faa

meta:map

*.faa:file

amps_tsv

meta:map

*.tsv:file

versions_ampir

${task.process}:string

ampir:string

Rscript -e "library(ampir); cat(paste((unlist(packageVersion('ampir'))), collapse = '.'))":eval

Topics

versions

${task.process}:string

ampir:string

Rscript -e "library(ampir); cat(paste((unlist(packageVersion('ampir'))), collapse = '.'))":eval

Tools

ampir GPL v2

included in

maintainer

get in touch

`meta`
`:map`

`faa`
`:file`

`model`
`:string`

`min_length`
`:integer`

`min_probability`
`:float`

`amps_faa`

`meta`
`:map`

`*.faa`
`:file`

`amps_tsv`

`meta`
`:map`

`*.tsv`
`:file`

`versions_ampir`

`${task.process}`
`:string`

`ampir`
`:string`

`Rscript -e "library(ampir); cat(paste((unlist(packageVersion('ampir'))), collapse = '.'))"`
`:eval`

`versions`

`${task.process}`
`:string`

`ampir`
`:string`

`Rscript -e "library(ampir); cat(paste((unlist(packageVersion('ampir'))), collapse = '.'))"`
`:eval`

ampir
GPL v2