count: 2
list:
- accessibility: Open access
  additionDate: '2018-12-12T12:35:31Z'
  biotoolsCURIE: biotools:bio.tools
  biotoolsID: bio.tools
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Contributors
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: https://biotools.readthedocs.io/en/latest/contributors.html
  description: The community registry of computational tools and data resources for
    biosciences.
  documentation:
  - note: API usage guide
    type:
    - API documentation
    url: https://biotools.readthedocs.io/en/latest/api_usage_guide.html
  - note: API Reference
    type:
    - API documentation
    url: https://biotools.readthedocs.io/en/latest/api_reference.html
  - note: null
    type:
    - Citation instructions
    url: https://biotools.readthedocs.io/en/latest/publications.html#citation
  - note: null
    type:
    - Contributions policy
    url: https://biotools.readthedocs.io/en/latest/contributors_guide.html
  - note: null
    type:
    - General
    url: https://biotools.readthedocs.io/en/latest/
  - note: null
    type:
    - Governance
    url: https://biotools.readthedocs.io/en/latest/governance.html
  - note: Curators Guide
    type:
    - User manual
    url: https://biotools.readthedocs.io/en/latest/curators_guide.html
  download:
  - note: null
    type: Source code
    url: https://github.com/bio-tools/biotoolsRegistry
    version: null
  editPermission:
    authors:
    - hans
    type: group
  elixirCommunity: []
  elixirNode:
  - Denmark
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Text
        uri: http://edamontology.org/data_3671
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    note: null
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output:
    - data:
        term: Tool metadata
        uri: http://edamontology.org/data_0958
      format:
      - term: YAML
        uri: http://edamontology.org/format_3750
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: XML
        uri: http://edamontology.org/format_2332
  homepage: https://bio.tools
  homepage_status: 0
  language:
  - JavaScript
  - Python
  lastUpdate: '2026-03-25T12:24:23.606945Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Helpdesk
    url: https://biotools.readthedocs.io/en/latest/support.html?highlight=help
  - note: null
    type:
    - Issue tracker
    url: https://github.com/bio-tools/biotoolsregistry/issues
  - note: null
    type:
    - Mailing list
    url: https://biotools.readthedocs.io/en/latest/contributors_guide.html#mailing-list
  - note: null
    type:
    - Repository
    url: https://github.com/bio-tools/biotoolsregistry/
  maturity: Emerging
  name: bio.tools
  operatingSystem: []
  otherID:
  - type: rrid
    value: RRID:SCR_014695
    version: null
  owner: jison
  publication:
  - doi: 10.1093/nar/gkv1116
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.12688/f1000research.12974.1
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  - doi: 10.1093/gigascience/gix022
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  - doi: 10.1007/s10009-015-0392-z
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web API
  - Database portal
  - Web application
  topic:
  - term: Ontology and terminology
    uri: http://edamontology.org/topic_0089
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-12-21T07:28:12Z'
  biotoolsCURIE: biotools:tooldog
  biotoolsID: tooldog
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Institut Pasteur
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://research.pasteur.fr
  - email: null
    fundrefid: null
    gridid: null
    name: C3BI
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole: []
    url: https://research.pasteur.fr/en/center/c3bi/
  - email: null
    fundrefid: null
    gridid: null
    name: Bioinformatics and Biostatistics Hub
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole:
    - Provider
    url: https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/
  - email: hmenager@pasteur.fr
    fundrefid: null
    gridid: null
    name: Hervé Ménager
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: kehillio@pasteur.fr
    fundrefid: null
    gridid: null
    name: Kenzo-Hugo Hillion
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: This tool aims to generate XML template for Galaxy or CWL from the
    description of tools from the bio.tools registry.
  documentation:
  - note: null
    type:
    - General
    url: http://tooldog.readthedocs.io/en/latest/?badge=latest
  download:
  - note: Download link to v.0.3.5
    type: Source code
    url: https://github.com/bio-tools/ToolDog/archive/v0.3.5.tar.gz
    version: null
  editPermission:
    authors:
    - hmenager
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Formatting
      uri: http://edamontology.org/operation_0335
    output:
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
      - term: YAML
        uri: http://edamontology.org/format_3750
  homepage: https://github.com/bio-tools/ToolDog
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2018-12-10T12:58:59Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/bio-tools/ToolDog
  maturity: Emerging
  name: ToolDog
  operatingSystem:
  - Linux
  otherID: []
  owner: khillion
  publication:
  - doi: 10.12688/f1000research.12974.1
    metadata:
      abstract: © 2017 Hillion KH et al.Workbench and workflow systems such as Galaxy,
        Taverna, Chipster, or Common Workflow Language (CWL)-based frameworks, facilitate
        the access to bioinformatics tools in a user-friendly, scalable and reproducible
        way. Still, the integration of tools in such environments remains a cumbersome,
        time consuming and error-prone process. A major consequence is the incomplete
        or outdated description of tools that are often missing important information,
        including parameters and metadata such as publication or links to documentation.
        ToolDog (Tool DescriptiOn Generator) facilitates the integration of tools
        - which have been registered in the ELIXIR tools registry (https://bio.tools)
        - into workbench environments by generating tool description templates. ToolDog
        includes two modules. The first module analyses the source code of the bioinformatics
        software with language-specific plugins, and generates a skeleton for a Galaxy
        XML or CWL tool description. The second module is dedicated to the enrichment
        of the generated tool description, using metadata provided by bio.tools. This
        last module can also be used on its own to complete or correct existing tool
        descriptions with missing metadata.
      authors:
      - name: Hillion K.-H.
      - name: Kuzmin I.
      - name: Khodak A.
      - name: Rasche E.
      - name: Crusoe M.
      - name: Peterson H.
      - name: Ison J.
      - name: Menager H.
      citationCount: 6
      date: '2017-01-01T00:00:00Z'
      journal: F1000Research
      title: Using bio.tools to generate and annotate workbench tool descriptions
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Ontology and terminology
    uri: http://edamontology.org/topic_0089
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 1
  version:
  - 0.3.5
next: null
previous: null
