nf-modules/modules/bigbio/thermorawfileparser/meta.yml at 47ebbd0739c1682e404584da5a459c131b896f56 · biosustain/nf-modules · GitHub

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name: thermorawfileparser
description: Convert RAW file to mzML or MGF files format
keywords:
  - raw
  - mzml
  - mgf
  - parquet
  - parser
  - proteomics
tools:
  - thermorawfileparser:
      description: |
        ThermoRawFileParser converts Thermo RAW files to open standard formats like mzML, producing indexed output files.
        Use `task.ext.args` to pass additional arguments, e.g.:
        - `-f=0` for MGF output, `-f=1` for mzML, `-f=2` for indexed mzML (default), `-f=3` for Parquet, `-f=4` for None
        - `-L` or `--msLevel=VALUE` to select MS levels (e.g., `-L=1,2` or `--msLevel=1-3`)
      homepage: https://github.com/compomics/ThermoRawFileParser
      documentation: https://github.com/compomics/ThermoRawFileParser
      tool_dev_url: https://github.com/compomics/ThermoRawFileParser"
      doi: "10.1021/acs.jproteome.9b00328"
      licence:
        - "Apache Software"
      identifier: biotools:ThermoRawFileParser
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. `[ id:'sample1', single_end:false ]`
    - raw:
        type: file
        description: Thermo RAW file
        pattern: "*.{raw,RAW}"
        ontologies: []
output:
  spectra:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. `[ id:'sample1', single_end:false ]`
      - "*.{mzML,mzML.gz,mgf,mgf.gz,parquet,parquet.gz}":
          type: file
          description: Mass spectra in open format
          pattern: "*.{mzML,mzML.gz,mgf,mgf.gz,parquet,parquet.gz}"
          ontologies: []
  versions_thermorawfileparser:
    - - ${task.process}:
          type: string
          description: The process the versions were collected from
      - thermorawfileparser:
          type: string
          description: The name of the tool
      - ThermoRawFileParser.sh --version:
          type: eval
          description: The expression to obtain the version of the tool
  log:
    - "*.log":
        type: file
        description: Log file from the conversion process
        pattern: "*.log"
        ontologies: []
topics:
  versions:
    - - ${task.process}:
          type: string
          description: The process the versions were collected from
      - thermorawfileparser:
          type: string
          description: The name of the tool
      - ThermoRawFileParser.sh --version:
          type: eval
          description: The expression to obtain the version of the tool
authors:
  - "@jonasscheid"
  - "@daichengxin"
  - "@ypriverol"
maintainers:
  - "@jonasscheid"
  - "@daichengxin"
  - "@ypriverol"