name: "bedtools_window"
namespace: "bedtools"
version: "main"
authors:
- name: "Robrecht Cannoodt"
  roles:
  - "author"
  - "maintainer"
  info:
    links:
      email: "robrecht@data-intuitive.com"
      github: "rcannood"
      orcid: "0000-0003-3641-729X"
      linkedin: "robrechtcannoodt"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Data Science Engineer"
    - name: "Open Problems"
      href: "https://openproblems.bio"
      role: "Core Member"
argument_groups:
- name: "Inputs"
  arguments:
  - type: "file"
    name: "--input_a"
    alternatives:
    - "-a"
    description: "Query file in BED, GFF, or VCF format.\n\n**Format:** BED, GFF,\
      \ or VCF file with genomic coordinates\n**Content:** Features around which windows\
      \ will be created\n**Usage:** Each feature becomes the center of a search window\n\
      **Requirements:** Must have valid genomic coordinates\n"
    info: null
    example:
    - "queries.bed"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--input_b"
    alternatives:
    - "-b"
    description: "Database file in BED, GFF, or VCF format.\n\n**Format:** BED, GFF,\
      \ or VCF file with genomic coordinates  \n**Content:** Features to search for\
      \ within windows around A\n**Usage:** Features overlapping windows around A\
      \ will be reported\n**Requirements:** Must have matching chromosome names with\
      \ file A\n"
    info: null
    example:
    - "annotations.bed"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    description: "Output file with overlapping feature pairs.\n\n**Format:** Tab-separated\
      \ file with entries from both input files\n**Content:** For each overlap, complete\
      \ records from both A and B files\n**Structure:** Columns from A file followed\
      \ by columns from B file\n**Size:** Number of lines depends on overlaps found\
      \ within windows\n"
    info: null
    example:
    - "windowed_overlaps.bed"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Window Options"
  arguments:
  - type: "integer"
    name: "--window_size"
    alternatives:
    - "-w"
    description: "Base pairs added upstream and downstream of each entry in A.\n\n\
      **Default:** 1000 bp\n**Usage:** Creates symmetrical windows around features\
      \ in A\n**Effect:** Extends search region by this amount in both directions\n\
      **Range:** Must be positive integer\n**Note:** Cannot be used with -l/-r options\n"
    info: null
    example:
    - 5000
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--left_window"
    alternatives:
    - "-l"
    description: "Base pairs added upstream (left) of each entry in A.\n\n**Default:**\
      \ 1000 bp\n**Usage:** Creates asymmetrical windows with custom upstream extension\n\
      **Effect:** Extends search region upstream by this amount\n**Range:** Must be\
      \ positive integer\n**Note:** Use with -r to create asymmetrical windows\n"
    info: null
    example:
    - 2000
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--right_window"
    alternatives:
    - "-r"
    description: "Base pairs added downstream (right) of each entry in A.\n\n**Default:**\
      \ 1000 bp\n**Usage:** Creates asymmetrical windows with custom downstream extension\n\
      **Effect:** Extends search region downstream by this amount\n**Range:** Must\
      \ be positive integer\n**Note:** Use with -l to create asymmetrical windows\n"
    info: null
    example:
    - 3000
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--strand_windows"
    alternatives:
    - "-sw"
    description: "Define left (-l) and right (-r) based on strand orientation.\n\n\
      **Usage:** For negative-strand features, -l adds bases downstream\n**Effect:**\
      \ Makes window extensions relative to feature orientation\n**Default:** false\
      \ (extensions are always relative to chromosome coordinates)\n**Requirement:**\
      \ Only works with -l and -r options, not with -w\n"
    info: null
    direction: "input"
- name: "Strand Options"
  arguments:
  - type: "boolean_true"
    name: "--same_strand"
    alternatives:
    - "-sm"
    description: "Only report overlaps between features on the same strand.\n\n**Usage:**\
      \ Restricts results to strand-specific overlaps\n**Effect:** Features must be\
      \ on identical strands to be reported\n**Default:** false (strand is ignored)\n\
      **Note:** Cannot be used with --opposite_strand\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--opposite_strand"
    alternatives:
    - "-Sm"
    description: "Only report overlaps between features on opposite strands.\n\n**Usage:**\
      \ Restricts results to antisense overlaps\n**Effect:** Features must be on opposite\
      \ strands to be reported\n**Default:** false (strand is ignored)\n**Note:**\
      \ Cannot be used with --same_strand\n"
    info: null
    direction: "input"
- name: "Output Options"
  arguments:
  - type: "boolean_true"
    name: "--unique"
    alternatives:
    - "-u"
    description: "Write the original A entry once if any overlaps found in B.\n\n\
      **Usage:** Reports existence of overlap without listing all B features\n**Effect:**\
      \ Each A feature appears at most once in output\n**Output:** Only A file columns,\
      \ no B file columns\n**Use case:** When you only need to know if overlap exists\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--count"
    alternatives:
    - "-c"
    description: "For each entry in A, report the number of overlaps with B.\n\n**Usage:**\
      \ Adds count column showing number of B features in window\n**Effect:** Each\
      \ A entry gets additional column with overlap count\n**Output:** Original A\
      \ columns plus count column\n**Values:** 0 for no overlaps, positive integers\
      \ for overlap count\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_overlaps"
    alternatives:
    - "-v"
    description: "Only report entries in A that have no overlaps with B.\n\n**Usage:**\
      \ Filters to show only A features with no nearby B features\n**Effect:** Inverse\
      \ of normal operation (like \"grep -v\")\n**Output:** Only A file columns for\
      \ features with no overlaps\n**Use case:** Finding isolated or unique features\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--header"
    description: "Print the header from the A file prior to results.\n\n**Usage:**\
      \ Preserves header information from input file A\n**Effect:** First line of\
      \ output will be the A file header\n**Default:** false (no header in output)\n\
      **Note:** Only applicable if A file contains header lines\n"
    info: null
    direction: "input"
- name: "BAM Options"
  arguments:
  - type: "file"
    name: "--input_bam"
    alternatives:
    - "-abam"
    description: "Input A file in BAM format instead of BED/GFF/VCF.\n\n**Format:**\
      \ Sorted BAM file with aligned reads\n**Usage:** Replaces -a option for BAM\
      \ input\n**Output:** Default output is BAM format\n**Requirements:** Must be\
      \ coordinate-sorted\n**Note:** Cannot be used together with --input_a\n"
    info: null
    example:
    - "alignments.bam"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--uncompressed_bam"
    alternatives:
    - "-ubam"
    description: "Write uncompressed BAM output when using BAM input.\n\n**Usage:**\
      \ Only applicable when using --input_bam\n**Effect:** Output BAM will be uncompressed\
      \ for faster writing\n**Default:** false (compressed BAM output)\n**Performance:**\
      \ Faster writing but larger file size\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--bed_output"
    alternatives:
    - "-bed"
    description: "Write output as BED format when using BAM input.\n\n**Usage:** Only\
      \ applicable when using --input_bam\n**Effect:** Converts BAM records to BED\
      \ format in output\n**Default:** false (BAM output when BAM input)\n**Format:**\
      \ Standard BED format with coordinates and names\n"
    info: null
    direction: "input"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Examine a \"window\" around each feature in A and report overlapping\
  \ features in B.\n\nFor each feature in file A, bedtools window searches for overlapping\
  \ features in \nfile B within a defined window around each feature in A. The window\
  \ can be \nsymmetrical (same distance upstream and downstream) or asymmetrical (different\
  \ \ndistances). For each overlap found, the complete entries from both files A and\
  \ B \nare reported.\n\nThis tool is particularly useful for:\n- Finding features\
  \ within a specific distance of target regions\n- Associating regulatory elements\
  \ with nearby genes\n- Creating annotation contexts around genomic features\n- Proximity-based\
  \ genomic analysis\n- Building feature neighborhoods for downstream analysis\n"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
- type: "file"
  path: "test_helpers.sh"
info: null
status: "enabled"
scope:
  image: "public"
  target: "public"
requirements:
  commands:
  - "bedtools"
  - "ps"
keywords:
- "genomics"
- "window"
- "proximity"
- "overlap"
- "annotation"
- "neighborhood"
- "bedtools"
license: "MIT"
references:
  doi:
  - "10.1093/bioinformatics/btq033"
links:
  repository: "https://github.com/arq5x/bedtools2"
  homepage: "https://bedtools.readthedocs.io/en/latest/content/tools/window.html"
  documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/window.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: "quay.io/biocontainers/bedtools:2.31.1--h13024bc_3"
  target_registry: "images.viash-hub.com"
  target_tag: "main"
  namespace_separator: "/"
  setup:
  - type: "docker"
    run:
    - "bedtools --version 2>&1 | head -1 | sed 's/.*bedtools v/bedtools: /' > /var/software_versions.txt"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/bedtools/bedtools_window/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_window"
  executable: "target/executable/bedtools/bedtools_window/bedtools_window"
  viash_version: "0.9.4"
  git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b"
  git_remote: "https://github.com/viash-hub/biobox"
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"
