 ```sh
agat_convert_embl2gff.pl --help
```
 
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|   Another GFF Analysis Toolkit (AGAT) - Version: v1.4.0                      |
|   https://github.com/NBISweden/AGAT                                          |
|   National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se         |
 ------------------------------------------------------------------------------


Name:
    agat_converter_embl2gff.pl

Description:
    The script takes an EMBL file as input, and will translate it in gff
    format.

Usage:
        agat_converter_embl2gff.pl --embl infile.embl [ -o outfile ]

Options:
    --embl  Input EMBL file that will be read

    --emblmygff3
            Bolean - Means that the EMBL flat file comes from the EMBLmyGFF3
            software. This is an EMBL format dedicated for submission and
            contains particularity to deal with. This parameter is needed to
            get a proper sequence id in the GFF3 from an embl made with
            EMBLmyGFF3.

    --primary_tag, --pt, -t
            List of "primary tag". Useful to discard or keep specific
            features. Multiple tags must be coma-separated.

    -d      Bolean - Means that primary tags provided by the option
            "primary_tag" will be discarded.

    -k      Bolean - Means that only primary tags provided by the option
            "primary_tag" will be kept.

    -o, --output, --out, --outfile or --gff
            Output GFF file. If no output file is specified, the output will
            be written to STDOUT.

    -c or --config
            String - Input agat config file. By default AGAT takes as input
            agat_config.yaml file from the working directory if any,
            otherwise it takes the orignal agat_config.yaml shipped with
            AGAT. To get the agat_config.yaml locally type: "agat config
            --expose". The --config option gives you the possibility to use
            your own AGAT config file (located elsewhere or named
            differently).

    -h or --help
            Display this helpful text.

Feedback:
  Did you find a bug?:
    Do not hesitate to report bugs to help us keep track of the bugs and
    their resolution. Please use the GitHub issue tracking system available
    at this address:

                https://github.com/NBISweden/AGAT/issues

     Ensure that the bug was not already reported by searching under Issues.
     If you're unable to find an (open) issue addressing the problem, open a new one.
     Try as much as possible to include in the issue when relevant:
     - a clear description,
     - as much relevant information as possible,
     - the command used,
     - a data sample,
     - an explanation of the expected behaviour that is not occurring.

  Do you want to contribute?:
    You are very welcome, visit this address for the Contributing
    guidelines:
    https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md
