```sh
agat_convert_sp_gff2gtf.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_sp_gff2gtf.pl

Description:
    The script aims to convert any GTF/GFF file into a proper GTF file. Full
    information about the format can be found here:
    https://agat.readthedocs.io/en/latest/gxf.html You can choose among 7
    different GTF types (1, 2, 2.1, 2.2, 2.5, 3 or relax). Depending the
    version selected the script will filter out the features that are not
    accepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene
    pseudogene) will be converted into gene feature and every level2 feature
    (e.g mRNA ncRNA) will be converted into transcript feature. Using the
    "relax" option you will produce a GTF-like output keeping all original
    feature types (3rd column). No modification will occur e.g. mRNA to
    transcript.

    To be fully GTF compliant all feature have a gene_id and a transcript_id
    attribute. The gene_id is unique identifier for the genomic source of
    the transcript, which is used to group transcripts into genes. The
    transcript_id is a unique identifier for the predicted transcript, which
    is used to group features into transcripts.

Usage:
        agat_convert_sp_gff2gtf.pl --gff infile.gff [ -o outfile ]
        agat_convert_sp_gff2gtf -h

Options:
    --gff, --gtf or -i
            Input GFF/GTF file that will be read

    --gtf_version version of the GTF output (1,2,2.1,2.2,2.5,3 or relax).
    Default value from AGAT config file (relax for the default config). The
    script option has the higher priority.
            relax: all feature types are accepted.

            GTF3 (9 feature types accepted): gene, transcript, exon, CDS,
            Selenocysteine, start_codon, stop_codon, three_prime_utr and
            five_prime_utr

            GTF2.5 (8 feature types accepted): gene, transcript, exon, CDS,
            UTR, start_codon, stop_codon, Selenocysteine

            GTF2.2 (9 feature types accepted): CDS, start_codon, stop_codon,
            5UTR, 3UTR, inter, inter_CNS, intron_CNS and exon

            GTF2.1 (6 feature types accepted): CDS, start_codon, stop_codon,
            exon, 5UTR, 3UTR

            GTF2 (4 feature types accepted): CDS, start_codon, stop_codon,
            exon

            GTF1 (5 feature types accepted): CDS, start_codon, stop_codon,
            exon, intron

    -o , --output , --out , --outfile or --gtf
            Output GTF 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

