name: "bedtools_pairtobed"
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: "--bedpe"
    alternatives:
    - "-a"
    description: "Input BEDPE file with paired interval data.\n\n**Format:** BEDPE\
      \ format with paired genomic coordinates\n**Content:** Each line represents\
      \ a pair of genomic intervals\n**Columns:** chrom1, start1, end1, chrom2, start2,\
      \ end2, [name], [score], [strand1], [strand2]\n**Usage:** Pairs will be tested\
      \ for overlaps with features in --bed file\n**Requirements:** Must be in valid\
      \ BEDPE format\n"
    info: null
    example:
    - "structural_variants.bedpe"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bed"
    alternatives:
    - "-b"
    description: "Input BED/GFF/VCF file with genomic features.\n\n**Format:** BED,\
      \ GFF, or VCF file with genomic coordinates\n**Content:** Genomic features to\
      \ test for overlaps with BEDPE pairs\n**Usage:** Features will be intersected\
      \ with paired intervals from --bedpe\n**Requirements:** Standard genomic coordinate\
      \ format\n"
    info: null
    example:
    - "genes.bed"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--bam_input"
    alternatives:
    - "-abam"
    description: "Input BAM file instead of BEDPE file.\n\n**Format:** BAM format\
      \ with paired-end alignments\n**Content:** Paired-end sequencing reads\n**Requirements:**\
      \ Must be grouped or sorted by query name\n**Usage:** Replaces --bedpe argument\
      \ when working with BAM input\n**Output:** Will produce BAM output by default\
      \ (unless --bedpe_output is used)\n"
    info: null
    example:
    - "paired_reads.bam"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    description: "Output file with overlap results.\n\n**Format:** Depends on input\
      \ type and options\n**BAM input:** BAM format (unless --bedpe_output specified)\n\
      **BEDPE input:** BEDPE format with overlapping pairs\n**Content:** Original\
      \ paired intervals that meet the overlap criteria\n"
    info: null
    example:
    - "overlapping_pairs.bedpe"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Output Options"
  arguments:
  - type: "boolean_true"
    name: "--uncompressed_bam"
    alternatives:
    - "-ubam"
    description: "Write uncompressed BAM output.\n\n**Usage:** Only applies when using\
      \ BAM input (--bam_input)\n**Default:** Compressed BAM output\n**Effect:** Produces\
      \ larger but faster-to-write output files\n**Applications:** When downstream\
      \ tools require uncompressed BAM\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--bedpe_output"
    alternatives:
    - "-bedpe"
    description: "Write output in BEDPE format when using BAM input.\n\n**Usage:**\
      \ Only applies when using BAM input (--bam_input)\n**Default:** BAM output when\
      \ BAM input is used\n**Effect:** Converts BAM pairs to BEDPE format in output\n\
      **Applications:** When you need text-based output from BAM input\n"
    info: null
    direction: "input"
- name: "Overlap Options"
  arguments:
  - type: "double"
    name: "--min_overlap"
    alternatives:
    - "-f"
    description: "Minimum overlap required as fraction of BEDPE intervals.\n\n**Default:**\
      \ 1E-9 (effectively 1 base pair)\n**Range:** 0.0 to 1.0\n**Usage:** Overlap\
      \ must be at least this fraction of the BEDPE interval\n**Example:** 0.5 requires\
      \ 50% overlap\n"
    info: null
    example:
    - 0.1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--type"
    description: "Approach for reporting overlaps between BEDPE and BED.\n\n**either:**\
      \ Report if either end of BEDPE overlaps BED (default)\n**neither:** Report\
      \ if neither end of BEDPE overlaps BED\n**both:** Report if both ends of BEDPE\
      \ overlap BED\n**xor:** Report if exactly one end of BEDPE overlaps BED\n**notboth:**\
      \ Report if neither or exactly one end overlaps (xor + neither)\n**ispan:**\
      \ Report overlaps between [end1, start2] span of BEDPE and BED\n**ospan:** Report\
      \ overlaps between [start1, end2] span of BEDPE and BED\n**notispan:** Report\
      \ if ispan doesn't overlap BED\n**notospan:** Report if ospan doesn't overlap\
      \ BED\n"
    info: null
    example:
    - "both"
    default:
    - "either"
    required: false
    choices:
    - "either"
    - "neither"
    - "both"
    - "xor"
    - "notboth"
    - "ispan"
    - "ospan"
    - "notispan"
    - "notospan"
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Strand Options"
  arguments:
  - type: "boolean_true"
    name: "--same_strand"
    alternatives:
    - "-s"
    description: "Require same strandedness when finding overlaps.\n\n**Default:**\
      \ Ignore strand information\n**Usage:** Only report overlaps on the same strand\n\
      **Note:** Not applicable with ispan, ospan, notispan, or notospan types\n**Applications:**\
      \ Strand-specific analyses\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--opposite_strand"
    alternatives:
    - "-S"
    description: "Require different strandedness when finding overlaps.\n\n**Default:**\
      \ Ignore strand information\n**Usage:** Only report overlaps on opposite strands\n\
      **Note:** Not applicable with ispan, ospan, notispan, or notospan types\n**Applications:**\
      \ Antisense interaction analyses\n"
    info: null
    direction: "input"
- name: "BAM-specific Options"
  arguments:
  - type: "boolean_true"
    name: "--edit_distance"
    alternatives:
    - "-ed"
    description: "Use BAM total edit distance (NM tag) for BEDPE score.\n\n**Default:**\
      \ Use minimum mapping quality of the two mates as score\n**Usage:** Only applies\
      \ when using BAM input (--bam_input)\n**Effect:** Reports total edit distance\
      \ from both mates as the score\n**Applications:** Quality assessment based on\
      \ sequence accuracy\n"
    info: null
    direction: "input"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Report overlaps between a BEDPE file and a BED/GFF/VCF file.\n\nbedtools\
  \ pairtobed finds overlaps between paired-end intervals (BEDPE format) \nand genomic\
  \ features in BED/GFF/VCF format. This tool is particularly useful \nfor analyzing\
  \ paired-end sequencing data, structural variants, or any genomic \ndata where you\
  \ need to consider relationships between paired intervals.\n\nThis tool is commonly\
  \ used for:\n- Annotating structural variants with genomic features\n- Finding overlaps\
  \ between paired-end ChIP-seq reads and genes\n- Analyzing chromatin interactions\
  \ (Hi-C, ChIA-PET) with genomic annotations\n- Quality control of paired-end sequencing\
  \ experiments\n- Intersecting BEDPE format data with reference annotations\n- Processing\
  \ BAM files with paired-end alignment information\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"
- "paired-end"
- "bedpe"
- "overlaps"
- "structural-variants"
- "bam"
- "intervals"
license: "MIT"
references:
  doi:
  - "10.1093/bioinformatics/btq033"
links:
  repository: "https://github.com/arq5x/bedtools2"
  homepage: "https://bedtools.readthedocs.io/en/latest/content/tools/pairtobed.html"
  documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/pairtobed.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\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/bedtools/bedtools_pairtobed/config.vsh.yaml"
  runner: "nextflow"
  engine: "docker|native"
  output: "target/nextflow/bedtools/bedtools_pairtobed"
  executable: "target/nextflow/bedtools/bedtools_pairtobed/main.nf"
  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"
