name: "agat_sp_filter_feature_from_kill_list"
namespace: "agat"
version: "add_sgdemux"
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:
    - "-f"
    - "--ref"
    - "--reffile"
    description: "Input GFF3 file that will be read."
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--kill_list"
    alternatives:
    - "--kl"
    description: "Text file containing the kill list. One value per line."
    info: null
    example:
    - "kill_list.txt"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    alternatives:
    - "-o"
    - "--out"
    description: "Path to the output GFF file that contains filtered features. \n"
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Arguments"
  arguments:
  - type: "string"
    name: "--type"
    alternatives:
    - "-p"
    - "-l"
    description: "Primary tag option, case insensitive, list. Allow to specify the\
      \ feature types that \nwill be handled. \n\nYou can specify a specific feature\
      \ by giving its primary tag name (column 3) as: \n\n  * cds\n  * Gene\n  * mRNA\n\
      \  \nYou can specify directly all the feature of a particular\nlevel: \n\n \
      \ * level2=mRNA,ncRNA,tRNA,etc \n  * level3=CDS,exon,UTR,etc. \n\nBy default\
      \ all features are taken into account. Fill the option with the value \"all\"\
      \ will \nhave the same behaviour.\n"
    info: null
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "string"
    name: "--attribute"
    alternatives:
    - "-a"
    description: "Attribute tag to specify the attribute to analyse. Case sensitive.\
      \ Default: ID\n"
    info: null
    example:
    - "ID"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--config"
    alternatives:
    - "-c"
    description: "AGAT config file. By default AGAT takes the original agat_config.yaml\
      \ shipped with AGAT.\nThe `--config` option gives you the possibility to use\
      \ your own AGAT config file (located \nelsewhere 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: ";"
  - type: "boolean_true"
    name: "--verbose"
    alternatives:
    - "-v"
    description: "Verbose option for debugging purpose."
    info: null
    direction: "input"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Remove features based on a kill list. The default behaviour is to look\
  \ at the features's ID. \nIf the feature has an ID (case insensitive) listed among\
  \ the kill list it will be removed.\nRemoving a level1 or level2 feature will automatically\
  \ remove all linked subfeatures, and \nremoving all children of a feature will automatically\
  \ remove this feature too.\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"
- "filtering"
- "gff"
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/en/latest/tools/agat_sp_filter_feature_from_kill_list.html"
  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: "add_sgdemux"
  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_sp_filter_feature_from_kill_list/config.vsh.yaml"
  runner: "nextflow"
  engine: "docker|native"
  output: "target/nextflow/agat/agat_sp_filter_feature_from_kill_list"
  executable: "target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf"
  viash_version: "0.9.0"
  git_commit: "402ad6a813c0d0b141bbf8f9a3aab9c270a74812"
  git_remote: "https://x-access-token:ghs_VWGBwCOTHxXRJ07uVE94xFn8UJ2FmS0FLhmc@github.com/viash-hub/biobox"
  git_tag: "v0.2.0-27-g402ad6a"
package_config:
  name: "biobox"
  version: "add_sgdemux"
  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 := 'add_sgdemux'"
  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"
