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biobox/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
CI 09f5294af0 Build branch main with version main (add1252) 
Build pipeline: viash-hub.biobox.main-bv4sf

Source commit: add125261c

Source message: FEAT: avoid using boolean_false (#160)
2024-10-07 09:26:30 +00:00

256 lines
8.3 KiB
YAML
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name: "agat_convert_sp_gff2gtf"
namespace: "agat"
version: "main"
authors:
- name: "Leïla Paquay"
roles:
- "author"
- "maintainer"
info:
links:
email: "leila@data-intuitive.com"
github: "Leila011"
linkedin: "leilapaquay"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Software Developer"
argument_groups:
- name: "Inputs"
arguments:
- type: "file"
name: "--gff"
alternatives:
- "-i"
description: "Input GFF/GTF file that will be read"
info: null
example:
- "input.gff"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Outputs"
arguments:
- type: "file"
name: "--output"
alternatives:
- "-o"
- "--out"
- "--outfile"
- "--gtf"
description: "Output GTF file. If no output file is specified, the output will\
\ be written to STDOUT."
info: null
example:
- "output.gtf"
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- name: "Arguments"
arguments:
- type: "string"
name: "--gtf_version"
description: "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. \n\n * relax: all feature types are accepted. \
\ \n * GTF3 (9 feature types accepted): gene, transcript, exon, CDS, Selenocysteine,\
\ start_codon, stop_codon, three_prime_utr and five_prime_utr. \n * GTF2.5\
\ (8 feature types accepted): gene, transcript, exon, CDS, UTR, start_codon,\
\ stop_codon, Selenocysteine. \n * GTF2.2 (9 feature types accepted): CDS,\
\ start_codon, stop_codon, 5UTR, 3UTR, inter, inter_CNS, intron_CNS and exon.\
\ \n * GTF2.1 (6 feature types accepted): CDS, start_codon, stop_codon, exon,\
\ 5UTR, 3UTR. \n * GTF2 (4 feature types accepted): CDS, start_codon, stop_codon,\
\ exon. \n * GTF1 (5 feature types accepted): CDS, start_codon, stop_codon,\
\ exon, intron. \n"
info: null
example:
- "3"
required: false
choices:
- "relax"
- "1"
- "2"
- "2.1"
- "2.2"
- "2.5"
- "3"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--config"
alternatives:
- "-c"
description: "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).\n"
info: null
example:
- "custom_agat_config.yaml"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
description: "The script aims to convert any GTF/GFF file into a proper GTF file.\
\ Full\ninformation about the format can be found here:\nhttps://agat.readthedocs.io/en/latest/gxf.html\
\ You can choose among 7\ndifferent GTF types (1, 2, 2.1, 2.2, 2.5, 3 or relax).\
\ Depending the\nversion selected the script will filter out the features that are\
\ not\naccepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene\npseudogene)\
\ will be converted into gene feature and every level2 feature\n(e.g mRNA ncRNA)\
\ will be converted into transcript feature. Using the\n\"relax\" option you will\
\ produce a GTF-like output keeping all original\nfeature types (3rd column). No\
\ modification will occur e.g. mRNA to\ntranscript.\n\nTo be fully GTF compliant\
\ all feature have a gene_id and a transcript_id\nattribute. The gene_id is unique\
\ identifier for the genomic source of\nthe transcript, which is used to group transcripts\
\ into genes. The\ntranscript_id is a unique identifier for the predicted transcript,\
\ which\nis used to group features into transcripts.\n"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
- type: "file"
path: "test_data"
info: null
status: "enabled"
requirements:
commands:
- "ps"
keywords:
- "gene annotations"
- "GTF conversion"
license: "GPL-3.0"
references:
doi:
- "10.5281/zenodo.3552717"
links:
repository: "https://github.com/NBISweden/AGAT"
homepage: "https://github.com/NBISweden/AGAT"
documentation: "https://agat.readthedocs.io/"
issue_tracker: "https://github.com/NBISweden/AGAT/issues"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "quay.io/biocontainers/agat:1.4.0--pl5321hdfd78af_0"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
run:
- "agat --version | sed 's/AGAT\\s\\(.*\\)/agat: \"\\1\"/' > /var/software_versions.txt\n"
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/agat/agat_convert_sp_gff2gtf/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/agat/agat_convert_sp_gff2gtf"
executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf"
viash_version: "0.9.0"
git_commit: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
git_tag: "v0.2.0-9-gadd1252"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"
- "sequencing"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/biobox"
issue_tracker: "https://github.com/viash-hub/biobox/issues"
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