modules/openms_fileconverter

Converts between different mass spectrometry file formats (e.g. mzML, mzXML, mgf, mzData, dta, dta2d, featureXML, consensusXML, idXML).

file conversionmass spectrometrymzmlmzxmlopenmsproteomics

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

Description

Converts between different mass spectrometry file formats (e.g. mzML, mzXML, mgf, mzData, dta, dta2d, featureXML, consensusXML, idXML).

Input

name:type

description

pattern

`meta`
`:map`

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

`input_file`
`:file`

Mass spectrometry data file in any OpenMS-supported input format

*.{mzML,mzXML,mgf,mzData,dta,dta2d,edta,featureXML,consensusXML,idXML,traML,fid,raw}

`out_type`
`:string`

Target output file extension/format (e.g. mzML, mgf, featureXML)

Output

name:type

description

pattern

`converted`

`meta`
`:map`

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

`${prefix}.${out_type}`
`:file`

Converted mass spectrometry file in the format specified via out_type

*.{mzML,mzXML,mgf,mzData,dta,dta2d,edta,featureXML,consensusXML,idXML,traML}

`versions_openms`

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

The name of the process

`openms`
`:string`

The name of the tool

`FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\1/p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`openms`
`:string`

The name of the tool

`FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\1/p'`
`:eval`

The expression to obtain the version of the tool

Tools

openms
BSD

OpenMS is an open-source software C++ library for LC-MS data management and analyses

openms.de openms.readthedocs.io/en/latest https://github.com/OpenMS/OpenMS 10.1038/s41592-024-02197-7

modules/openms_fileconverter

Description

Input

`meta`
`:map`

`input_file`
`:file`

`out_type`
`:string`

Output

`converted`

`meta`
`:map`

`${prefix}.${out_type}`
`:file`

`versions_openms`

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

`openms`
`:string`

`FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\1/p'`
`:eval`

Topics

`versions`

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

`openms`
`:string`

`FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\1/p'`
`:eval`

Tools

openms
BSD

included in

maintainer

get in touch

modules/openms_fileconverter

Description

Input

meta:map

input_file:file

out_type:string

Output

converted

meta:map

${prefix}.${out_type}:file

versions_openms

${task.process}:string

openms:string

FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\1/p':eval

Topics

versions

${task.process}:string

openms:string

FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\1/p':eval

Tools

openms BSD

included in

maintainer

get in touch

`meta`
`:map`

`input_file`
`:file`

`out_type`
`:string`

`converted`

`meta`
`:map`

`${prefix}.${out_type}`
`:file`

`versions_openms`

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

`openms`
`:string`

`FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\1/p'`
`:eval`

`versions`

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

`openms`
`:string`

`FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\1/p'`
`:eval`

openms
BSD