biobox/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml

name: "bedtools_bamtobed"
namespace: "bedtools"
version: "main"
authors:
- name: "Theodoro Gasperin Terra Camargo"
  roles:
  - "author"
  - "maintainer"
  info:
    links:
      email: "theodorogtc@gmail.com"
      github: "tgaspe"
      linkedin: "theodoro-gasperin-terra-camargo"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Bioinformatician"
argument_groups:
- name: "Inputs"
  arguments:
  - type: "file"
    name: "--input"
    alternatives:
    - "-i"
    description: "Input BAM file."
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    alternatives:
    - "-o"
    description: "Output BED file."
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Options"
  arguments:
  - type: "boolean_true"
    name: "--bedpe"
    description: "Write BEDPE format. Requires BAM to be grouped or sorted by query.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--mate1"
    description: "When writing BEDPE (-bedpe) format, always report mate one as the\
      \ first BEDPE \"block\".\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--bed12"
    description: "Write \"blocked\" BED format (aka \"BED12\"). Forces -split.\nSee\
      \ http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--split"
    description: "Report \"split\" BAM alignments as separate BED entries.\nSplits\
      \ only on N CIGAR operations.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--splitD"
    description: "Split alignments based on N and D CIGAR operators.\nForces -split.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--edit_distance"
    alternatives:
    - "-ed"
    description: "Use BAM edit distance (NM tag) for BED score.\n- Default for BED\
      \ is to use mapping quality.\n- Default for BEDPE is to use the minimum of\n\
      \  the two mapping qualities for the pair.\n- When -ed is used with -bedpe,\
      \ the total edit\n  distance from the two mates is reported.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--tag"
    description: "Use other NUMERIC BAM alignment tag for BED score.\nDefault for\
      \ BED is to use mapping quality. Disallowed with BEDPE output.\n"
    info: null
    example:
    - "SM"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--color"
    description: "An R,G,B string for the color used with BED12 format.\nDefault is\
      \ (255,0,0).\n"
    info: null
    example:
    - "250,250,250"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--cigar"
    description: "Add the CIGAR string to the BED entry as a 7th column.\n"
    info: null
    direction: "input"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Converts BAM alignments to BED6 or BEDPE format."
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
- type: "file"
  path: "test_data"
info: null
status: "enabled"
scope:
  image: "public"
  target: "public"
requirements:
  commands:
  - "ps"
keywords:
- "Converts"
- "BAM"
- "BED"
- "BED6"
- "BEDPE"
license: "MIT"
references:
  doi:
  - "10.1093/bioinformatics/btq033"
links:
  repository: "https://github.com/arq5x/bedtools2"
  homepage: "https://bedtools.readthedocs.io/en/latest/#"
  documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html"
  issue_tracker: "https://github.com/arq5x/bedtools2/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: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
  target_tag: "main"
  namespace_separator: "/"
  setup:
  - type: "apt"
    packages:
    - "bedtools"
    - "procps"
    interactive: false
  - type: "docker"
    run:
    - "echo \"bedtools: \\\"$(bedtools --version | sed -n 's/^bedtools //p')\\\"\"\
      \ > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/bedtools/bedtools_bamtobed/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_bamtobed"
  executable: "target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed"
  viash_version: "0.9.4"
  git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
  git_remote: "https://github.com/viash-hub/biobox"
  git_tag: "v0.2.0-32-gc733de2"
package_config:
  name: "biobox"
  version: "main"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.4"
  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"