Annotate command reference

The s4n annotate command is used to annotate CWL files with metadata (see CWL documentation: Metadata and Authorship and ARC CWL Metadata). It is recommended to annotate CWL files with minimal information.

Annotate CWL files

Usage: s4n annotate [TOOL_NAME] [COMMAND]

Commands:
  name         Annotates name of a tool or workflow
  description  Annotates description of a tool or workflow
  license      Annotates license of a tool or workflow
  schema       Annotates schema of a tool or workflow
  namespace    Annotates namespace of a tool or workflow
  author       Annotates author of a tool or workflow (schema.org)
  contributor  Annotates contributor of a tool or workflow (schema.org)
  performer    Annotates performer of a tool or workflow (arc ontology)
  process      Annotates a process (arc ontolology)
  container    Annotates container information of a tool or workflow
  custom       Annotates a CWL file with an custom field and value
  help         Print this message or the help of the given subcommand(s)

  Arguments:
    [TOOL_NAME]  Name of the tool or workflow to annotate

`annotate name`

The s4n annotate name command annotates a CWL file with a label.

Annotates name of a tool or workflow

Usage: s4n annotate name --name <NAME> <CWL_NAME>

Arguments:
  <CWL_NAME>  Name of the CWL file

Options:
  -n, --name <NAME>  Name of the tool or workflow
  -h, --help         Print help

 s4n annotate name main -n "An example tool demonstrating metadata."

The command will annotate a main.cwl with label “An example tool demonstrating metadata.”.

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: CommandLineTool

label: An example tool demonstrating metadata.

`annotate description`

The s4n annotate description command annotates a CWL file with a description.

Annotates description of a tool or workflow

Usage: s4n annotate description --description <DESCRIPTION> <CWL_NAME>

Arguments:
  <CWL_NAME>  Name of the CWL file

Options:
  -d, --description <DESCRIPTION>  Description of the tool or workflow
  -h, --help                       Print help

 s4n annotate description main -d "A description for my example tool"

The command will annotate main.cwl with doc “A description for my example tool”.

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: CommandLineTool

doc: A description for my example tool

`annotate license`

The s4n annotate license command annotates a CWL file with a license.

Annotates license of a tool or workflow

Usage: s4n annotate license --license <LICENSE> <CWL_NAME>

Arguments:
  <CWL_NAME>  Name of the CWL file

Options:
  -l, --license <LICENSE>  License of the tool or workflow
  -h, --help               Print help

 s4n annotate license main -l "MIT"

The command will annotate main.cwl with the MIT license.

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: CommandLineTool

s:license: MIT

$namespaces:
  s: https://schema.org/

$schemas:
  - https://schema.org/version/latest/schemaorg-current-https.rdf

`annotate schema`

The s4n annotate schema command annotates a CWL file with a schema.

Annotates schema of a tool or workflow

Usage: s4n annotate schema --schema <SCHEMA> <CWL_NAME>

Arguments:
  <CWL_NAME>  Name of the CWL file

Options:
  -s, --schema <SCHEMA>  Schema to annotate
  -h, --help             Print help

 s4n annotate schema main -s "https://schema.org/version/latest/schemaorg-current-https.rdf"

The command will annotate main.cwl with the schema.org schema.

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: CommandLineTool

$schemas:
  - https://schema.org/version/latest/schemaorg-current-https.rdf

`annotate namespace`

The s4n annotate namespace command annotates a CWL file with a namespace.

Annotates schema of a tool or workflow

Usage: s4n annotate namespace [OPTIONS] --namespace <NAMESPACE> <CWL_NAME>

Arguments:
  <CWL_NAME>  Name of the CWL file

Options:
  -n, --namespace <NAMESPACE>  Namespace to annotate
  -s, --short <SHORT>          Namespace abbreviation to annotate
  -h, --help                   Print help

 s4n annotate namespace main -n "http://edamontology.org/" -s "edam"

The command will annotate main.cwl with the edam namespace.

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: CommandLineTool

$namespaces:
  edam: http://edamontology.org/

`annotate author`

The s4n annotate author command annotates a CWL file with author information (based on schema.org). The minimum requirement is providing a name for the author, the other fields are optional. If the schema.org namespace and schema are not yet present, they are added to the CWL file.

Annotates author of a tool or workflow (schema.org)

Usage: s4n annotate author [OPTIONS] --name <NAME> <CWL_NAME>

Arguments:
  <CWL_NAME>  Name of the CWL file

Options:
  -n, --name <NAME>  Name of the person
  -m, --mail <MAIL>  Email of the person
  -i, --id <ID>      Identifier of the person, e.g., ORCID
  -h, --help         Print help

 s4n annotate author main -n "Jane Doe" -m "doe@mail.de" -i "https://orcid.org/0000-0000-0000-0000"

The command will annotate main.cwl with author Jane Doe.

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: CommandLineTool

s:author:
  - class: s:Person
    s:identifier: https://orcid.org/0000-0000-0000-0000
    s:email: mailto:doe@mail.de
    s:name: Jane Doe

$namespaces:
  s: https://schema.org/

$schemas:
  - https://schema.org/version/latest/schemaorg-current-https.rdf

`annotate contributor`

The s4n annotate contributor command annotates a CWL file with contributor information (based on schema.org). The fields are similar to the author fields. If the schema.org namespace and schema are not yet present, they are added to the CWL file.

Annotates author of a tool or workflow (schema.org)

Usage: s4n annotate contributor [OPTIONS] --name <NAME> <CWL_NAME>

Arguments:
  <CWL_NAME>  Name of the CWL file

Options:
  -n, --name <NAME>  Name of the person
  -m, --mail <MAIL>  Email of the person
  -i, --id <ID>      Identifier of the person, e.g., ORCID
  -h, --help         Print help

 s4n annotate contributor main -n "John Doe" -m "jdoe@mail.de" -i "http://orcid.org/0000-0000-0000-0001"

The command will annotate main.cwl with contributor John Doe.

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: CommandLineTool

s:contributor:
  - class: s:Person
    s:identifier: https://orcid.org/0000-0000-0000-0001
    s:email: mailto:jdoe@mail.de
    s:name: John Doe

$namespaces:
s: https://schema.org/

$schemas:
  - https://schema.org/version/latest/schemaorg-current-https.rdf

`annotate performer`

The s4n annotate performer command annotates a CWL file with performer information (based on ARC schema). A performer can be an individual or team behind the development or execution of the workflow. The minimum requirement is providing a first and a last name for the performer, the other fields are optional. The role field can be annotated with an ontology. If the ARC namespace and schema are not yet present, they are added to the CWL file.

Annotates performer of a tool or workflow (arc ontology)

Usage: s4n annotate performer [OPTIONS] --first_name <FIRST_NAME> --last_name <LAST_NAME> <CWL_NAME>

Arguments:
  <CWL_NAME>  Name of the CWL file

Options:
  -f, --first_name <FIRST_NAME>    First name of the performer
  -l, --last_name <LAST_NAME>      Last name of the performer
  -m, --mail <MAIL>                Email of the performer
  -a, --affiliation <AFFILIATION>  Affiliation of the performer
  -r, --role <ROLE>                Role of the performer
  -h, --help                       Print help

 s4n annotate performer main -f "John" -l "Doe" -m "jdoe@mail.de" -a "Institution1" -r "data scientist"

The command will annotate main.cwl with performer John Doe.

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: CommandLineTool

arc:performer:
- class: arc:Person
  arc:first name: John
  arc:last name: Doe
  arc:email: jdoe@mail.de
  arc:affiliation: Institution1
  arc:has role:
  - class: arc:role
    arc:term accession: http://purl.obolibrary.org/obo/OCCO_15205100
    arc:annotation value: data scientist

$namespaces:
  arc: https://github.com/nfdi4plants/ARC_ontology

$schemas:
  - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl

`annotate process`

The s4n annotate process command annotates a CWL file with a process sequence (based on ARC CWL Metadata). The parameter and value field can be annotated with an ontology. The minimum requirement is providing a name for the process sequence, the other fields are optional. If the ARC namespace and schema are not yet present, they are added to the CWL file.

Annotates a process sequence (arc ontolology)

Usage: s4n annotate process [OPTIONS] --name <NAME> <CWL_NAME>

Arguments:
  <CWL_NAME>  Name of the CWL file

Options:
  -n, --name <NAME>            Name of the process sequence step
  -i, --input <INPUT>          Input file or directory, e.g., folder/input.txt
  -o, --output <OUTPUT>        Output file or directory, e.g., folder/output.txt
  -p, --parameter <PARAMETER>  Process step parameter
  -v, --value <VALUE>          Process step value
  -h, --help                   Print help

 s4n annotate process main -n "script.py" -i "data/input.txt" -o "results/output.txt" -p "Data transformation" -v "Addition"

The command will annotate main.cwl with process sequence “script.py” with provided inputs, outputs, parameter and value.

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: CommandLineTool

arc:has process sequence:
- class: arc:process sequence
  arc:name: script.py
  arc:has input:
  - class: arc:data
    arc:name: data/input.txt
  arc:has output:
  - class: arc:data
    arc:name: results/output.txt
  arc:has parameter value:
  - class: arc:process parameter value
    arc:has parameter:
    - class: arc:protocol parameter
      arc:has parameter name:
      - class: arc:parameter name
        arc:term accession: http://purl.obolibrary.org/obo/NCIT_C43582
        arc:term source REF: ncit
        arc:annotation value: Data Transformation
  arc:value:
    - class: arc:ontology annotation
      arc:term accession: http://purl.obolibrary.org/obo/REX_0000089
      arc:term source REF: rex
      arc:annotation value: addition

$namespaces:
  arc: https://github.com/nfdi4plants/ARC_ontology

$schemas:
  - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl

`annotate container`

The s4n annotate container command annotates a CWL file with container information.

Annotates container information of a tool or workflow

Usage: s4n annotate container --container <CONTAINER> <CWL_NAME>

Arguments:
  <CWL_NAME> Name of the CWL file

Options:
  -c, --container <CONTAINER>  Annotation value for the container
  -h, --help                   Print help

 s4n annotate container main -c "Docker container"

The command will annotate main.cwl with the container annotation “Docker container”.

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: CommandLineTool

arc:has technology type:
- class: arc:technology type
  arc:annotation value: Docker container

$namespaces:
  arc: https://github.com/nfdi4plants/ARC_ontology

$schemas:
  - https://raw.githubusercontent.com/nfdi4plants/ARC_ontology/main/ARC_v2.0.owl

`annotate custom`

The s4n annotate custom command annotates a CWL file with a custom field and value.

Annotates a CWL file with an custom field and value

Usage: s4n annotate custom <CWL_NAME> <FIELD> <VALUE>

Arguments:
  <CWL_NAME>  Name of the CWL file
  <FIELD>     Field to annotate
  <VALUE>     Value for the field

Options:
  -h, --help  Print help

 s4n annotate custom main "s:programmingLanguage" "python"

The command will annotate main.cwl with programmingLanguage python.

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: CommandLineTool

s:programmingLanguage: python