name: "bedtools_intersect"
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_a"
    alternatives:
    - "-a"
    description: "The input file (BED/GFF/VCF/BAM) to be used as the -a file.\n"
    info: null
    example:
    - "input_a.bed"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--input_b"
    alternatives:
    - "-b"
    description: "The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s).\n"
    info: null
    example:
    - "input_b.bed"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    description: "The output BED file. \n"
    info: null
    example:
    - "output.bed"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Options"
  arguments:
  - type: "boolean_true"
    name: "--write_a"
    alternatives:
    - "-wa"
    description: "Write the original A entry for each overlap."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--write_b"
    alternatives:
    - "-wb"
    description: "Write the original B entry for each overlap. \nUseful for knowing\
      \ _what_ A overlaps. Restricted by -f and -r.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--left_outer_join"
    alternatives:
    - "-loj"
    description: "Perform a \"left outer join\". That is, for each feature in A report\
      \ each overlap with B. \nIf no overlaps are found, report a NULL feature for\
      \ B.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--write_overlap"
    alternatives:
    - "-wo"
    description: "Write the original A and B entries plus the number of base pairs\
      \ of overlap between the two features.\n- Overlaps restricted by -f and -r.\
      \ \n  Only A features with overlap are reported.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--write_overlap_plus"
    alternatives:
    - "-wao"
    description: "Write the original A and B entries plus the number of base pairs\
      \ of overlap between the two features.\n- Overlaps restricted by -f and -r.\
      \ \n  However, A features w/o overlap are also reported with a NULL B feature\
      \ and overlap = 0.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--report_A_if_no_overlap"
    alternatives:
    - "-u"
    description: "Write the original A entry _if_ no overlap is found. \n- In other\
      \ words, just report the fact >=1 hit was found.\n- Overlaps restricted by -f\
      \ and -r. \n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--number_of_overlaps_A"
    alternatives:
    - "-c"
    description: "For each entry in A, report the number of overlaps with B.\n- Reports\
      \ 0 for A entries that have no overlap with B.\n- Overlaps restricted by -f\
      \ and -r.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--report_no_overlaps_A"
    alternatives:
    - "-v"
    description: "Only report those entries in A that have _no overlaps_ with B.\n\
      - Similar to \"grep -v\" (an homage).\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--uncompressed_bam"
    alternatives:
    - "-ubam"
    description: "Write uncompressed BAM output. Default writes compressed BAM."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--same_strand"
    alternatives:
    - "-s"
    description: "Require same strandedness.  That is, only report hits in B.\nthat\
      \ overlap A on the _same_ strand.\n- By default, overlaps are reported without\
      \ respect to strand.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--opposite_strand"
    alternatives:
    - "-S"
    description: "Require different strandedness.  That is, only report hits in B\n\
      that overlap A on the _opposite_ strand.\n- By default, overlaps are reported\
      \ without respect to strand.\n"
    info: null
    direction: "input"
  - type: "double"
    name: "--min_overlap_A"
    alternatives:
    - "-f"
    description: "Minimum overlap required as a fraction of A.\n- Default is 1E-9\
      \ (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n"
    info: null
    example:
    - 0.5
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "double"
    name: "--min_overlap_B"
    alternatives:
    - "-F"
    description: "Minimum overlap required as a fraction of B.\n- Default is 1E-9\
      \ (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n"
    info: null
    example:
    - 0.5
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--reciprocal_overlap"
    alternatives:
    - "-r"
    description: "Require that the fraction overlap be reciprocal for A AND B.\n-\
      \ In other words, if -f is 0.90 and -r is used, this requires\nthat B overlap\
      \ 90% of A and A _also_ overlaps 90% of B.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--either_overlap"
    alternatives:
    - "-e"
    description: "Require that the minimum fraction be satisfied for A OR B.\n- In\
      \ other words, if -e is used with -f 0.90 and -F 0.10 this requires\nthat either\
      \ 90% of A is covered OR 10% of B is covered.\nWithout -e, both fractions would\
      \ have to be satisfied.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--split"
    description: "Treat \"split\" BAM or BED12 entries as distinct BED intervals."
    info: null
    direction: "input"
  - type: "file"
    name: "--genome"
    alternatives:
    - "-g"
    description: "Provide a genome file to enforce consistent chromosome \nsort order\
      \ across input files. Only applies when used \nwith -sorted option.\n"
    info: null
    example:
    - "genome.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--nonamecheck"
    description: "For sorted data, don't throw an error if the file \nhas different\
      \ naming conventions for the same chromosome \n(e.g., \"chr1\" vs \"chr01\"\
      ).\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--sorted"
    description: "Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--names"
    description: "When using multiple databases, provide an alias \nfor each that\
      \ will appear instead of a fileId when \nalso printing the DB record.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--filenames"
    description: "When using multiple databases, show each complete filename instead\
      \ of a fileId when also printing the DB record."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--sortout"
    description: "When using multiple databases, sort the output DB hits for each\
      \ record."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--bed"
    description: "If using BAM input, write output as BED."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--header"
    description: "Print the header from the A file prior to results."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_buffer_output"
    alternatives:
    - "--nobuf"
    description: "Disable buffered output. Using this option will cause each line\n\
      of output to be printed as it is generated, rather than saved\nin a buffer.\
      \ This will make printing large output files \nnoticeably slower, but can be\
      \ useful in conjunction with\nother software tools and scripts that need to\
      \ process one\nline of bedtools output at a time.\n"
    info: null
    direction: "input"
  - type: "integer"
    name: "--io_buffer_size"
    alternatives:
    - "--iobuf"
    description: "Specify amount of memory to use for input buffer.\nTakes an integer\
      \ argument. Optional suffixes K/M/G supported.\nNote: currently has no effect\
      \ with compressed files.       \n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "bedtools intersect allows one to screen for overlaps between two sets\
  \ of genomic features. \nMoreover, it allows one to have fine control as to how\
  \ the intersections are reported. \nbedtools intersect works with both BED/GFF/VCF\
  \ and BAM files as input.\n"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
info: null
status: "enabled"
scope:
  image: "public"
  target: "public"
requirements:
  commands:
  - "ps"
keywords:
- "feature intersection"
- "BAM"
- "BED"
- "GFF"
- "VCF"
license: "GPL-2.0, MIT"
references:
  doi:
  - "10.1093/bioinformatics/btq033"
links:
  repository: "https://github.com/arq5x/bedtools2"
  documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html"
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_intersect/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_intersect"
  executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
  viash_version: "0.9.4"
  git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
  git_remote: "https://github.com/viash-hub/biobox"
  git_tag: "v0.2.0-35-gb0db228"
package_config:
  name: "biobox"
  version: "main"
  summary: "A curated collection of high-quality, standalone bioinformatics components\
    \ built with [Viash](https://viash.io).\n"
  description: "`biobox` offers a suite of reliable bioinformatics components, similar\
    \ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
    \ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
    \ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
    \ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
    \ Run components directly via the command line or seamlessly integrate them into\
    \ Nextflow workflows.\n* **High Quality Standards:**\n    * Comprehensive documentation\
    \ for components and parameters.\n    * Full exposure of underlying tool arguments.\n\
    \    * Containerized (Docker) for dependency management and reproducibility.\n\
    \    * Unit tested for verified functionality.\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"