agat/agat_convert_embl2gff

gene annotations

GFF conversion

Description

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

Type

bash_script

License

GPL-3.0

Keywords

gene annotations

GFF conversion

Links

Repository

Issues

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.gff"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.0 \  
  -main-script target/nextflow/agat/agat_convert_embl2gff/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--embl	file required	Input EMBL file that will be read.

Name

Type & Properties

--embl

file

required

Outputs

Name	Type & Properties	Description
--output -o --out --outfile --gff	file output	Output GFF file. If no output file is specified, the output will be written to STDOUT.

Name

Type & Properties

--output

-o

--out

--outfile

--gff

file

output

Arguments

Name	Type & Properties	Description
--emblmygff3	boolean_true	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	string multiple	List of "primary tag". Useful to discard or keep specific features. Multiple tags must be comma-separated.
--discard -d	boolean_true	Means that primary tags provided by the option "primary_tag" will be discarded.
--keep -k	boolean_true	Means that only primary tags provided by the option "primary_tag" will be kept.
--config -c	file	Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original 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).

Name

Type & Properties

--emblmygff3

boolean_true

--primary_tag

--pt

-t

string

multiple

--discard

-d

boolean_true

--keep

-k

boolean_true

--config

-c

file