```sh
agat_convert_bed2gff.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_convert_bed2gff.pl

Description:
    The script takes a bed file as input, and will translate it in gff
    format. The BED format is described here:
    https://genome.ucsc.edu/FAQ/FAQformat.html#format1 The script converts
    0-based, half-open [start-1, end) bed file to 1-based, closed [start,
    end] General Feature Format v3 (GFF3).

Usage:
        agat_convert_bed2gff.pl --bed infile.bed [ -o outfile ]
        agat_convert_bed2gff.pl -h

Options:
    --bed   Input bed file that will be converted.

    --source
            The source informs about the tool used to produce the data and
            is stored in 2nd field of a gff file. Example:
            Stringtie,Maker,Augustus,etc. [default: data]

    --primary_tag
            The primary_tag corresponds to the data type and is stored in
            3rd field of a gff file. Example: gene,mRNA,CDS,etc. [default:
            gene]

    --inflate_off
            By default we inflate the block fields (blockCount, blockSizes,
            blockStarts) to create subfeatures of the main feature
            (primary_tag). The type of subfeature created is based on the
            inflate_type parameter. If you do not want this inflating
            behaviour you can deactivate it by using the --inflate_off
            option.

    --inflate_type
            Feature type (3rd column in gff) created when inflate parameter
            activated [default: exon].

    --verbose
            add verbosity

    -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
