name: "bedtools_fisher"
namespace: "bedtools"
version: "main"
authors:
- name: "Robrecht Cannoodt"
  roles:
  - "author"
  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: "First input file for comparison.\n\n**Format:** BED, GFF, VCF file\
      \ with genomic intervals\n**Requirement:** Must be sorted by chromosome, then\
      \ start position\n**Usage:** File A for Fisher's exact test comparison\n"
    info: null
    example:
    - "intervals_a.bed"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--input_b"
    alternatives:
    - "-b"
    description: "Second input file for comparison.\n\n**Format:** BED, GFF, VCF file\
      \ with genomic intervals\n**Requirement:** Must be sorted by chromosome, then\
      \ start position\n**Usage:** File B for Fisher's exact test comparison\n"
    info: null
    example:
    - "intervals_b.bed"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--genome"
    alternatives:
    - "-g"
    description: "Genome file defining chromosome sizes.\n\n**Format:** Tab-delimited\
      \ file with chromosome name and size\n**Purpose:** Enforces consistent chromosome\
      \ sort order\n**Example:** chr1\\t249250621\n"
    info: null
    example:
    - "genome.txt"
    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 Fisher's exact test results.\n\nContains statistical\
      \ results including p-values for overlap\nsignificance between input files.\n"
    info: null
    example:
    - "fisher_results.txt"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Overlap Options"
  arguments:
  - type: "boolean_true"
    name: "--merge_overlaps"
    alternatives:
    - "-m"
    description: "Merge overlapping intervals before analysis.\n\n**Effect:** Collapses\
      \ overlapping intervals in both files\n**Usage:** Prevents double-counting of\
      \ overlapping features\n**Default:** false (no merging)\n"
    info: null
    direction: "input"
  - type: "double"
    name: "--min_overlap_a"
    alternatives:
    - "-f"
    description: "Minimum overlap required as fraction of A.\n\n**Range:** 0.0 to\
      \ 1.0\n**Default:** 1E-9 (effectively 1bp)\n**Example:** 0.50 requires 50% of\
      \ A to be overlapped\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 fraction of B.\n\n**Range:** 0.0 to\
      \ 1.0\n**Default:** 1E-9 (effectively 1bp)\n**Example:** 0.50 requires 50% of\
      \ B to be overlapped\n"
    info: null
    example:
    - 0.5
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--reciprocal"
    alternatives:
    - "-r"
    description: "Require reciprocal overlap for both A and B.\n\n**Effect:** Both\
      \ -f and -F thresholds must be satisfied\n**Example:** With -f 0.90 -r, requires\
      \ B overlaps 90% of A AND A overlaps 90% of B\n**Default:** false\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--either"
    alternatives:
    - "-e"
    description: "Require minimum fraction satisfied for A OR B.\n\n**Effect:** Only\
      \ one of -f or -F thresholds needs to be satisfied\n**Alternative:** Without\
      \ -e, both fractions must be satisfied\n**Default:** false (both required)\n"
    info: null
    direction: "input"
- name: "Strand Options"
  arguments:
  - type: "boolean_true"
    name: "--same_strand"
    alternatives:
    - "-s"
    description: "Require same strandedness for overlaps.\n\n**Effect:** Only report\
      \ overlaps on the same strand\n**Default:** false (strand-independent)\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--opposite_strand"
    alternatives:
    - "-S"
    description: "Require different strandedness for overlaps.\n\n**Effect:** Only\
      \ report overlaps on opposite strands\n**Default:** false (strand-independent)\n"
    info: null
    direction: "input"
- name: "Format Options"
  arguments:
  - type: "boolean_true"
    name: "--split"
    description: "Treat split BAM or BED12 entries as distinct intervals.\n\n**Effect:**\
      \ Split multi-block entries into individual intervals\n**Usage:** For BAM alignments\
      \ with gaps or BED12 entries\n**Default:** false\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--bed_output"
    alternatives:
    - "--bed"
    description: "Write output in BED format when using BAM input.\n\n**Effect:**\
      \ Forces BED output format for BAM inputs\n**Default:** false\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--header"
    description: "Print header from file A prior to results.\n\n**Effect:** Includes\
      \ original header from input file A\n**Default:** false\n"
    info: null
    direction: "input"
- name: "Advanced Options"
  arguments:
  - type: "boolean_true"
    name: "--no_name_check"
    alternatives:
    - "--nonamecheck"
    description: "Skip chromosome naming convention checks for sorted data.\n\n**Effect:**\
      \ Allows different naming (e.g., \"chr1\" vs \"chr01\")\n**Usage:** For files\
      \ with inconsistent chromosome naming\n**Default:** false (strict checking)\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_buffer"
    alternatives:
    - "--nobuf"
    description: "Disable buffered output.\n\n**Effect:** Print each line immediately\
      \ instead of buffering\n**Usage:** For real-time processing or piping\n**Trade-off:**\
      \ Slower performance but immediate output\n**Default:** false (buffered output)\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--io_buffer"
    alternatives:
    - "--iobuf"
    description: "Specify input buffer memory size.\n\n**Format:** Integer with optional\
      \ K/M/G suffix\n**Example:** \"128M\" for 128 megabytes\n**Note:** No effect\
      \ with compressed files\n"
    info: null
    example:
    - "128M"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Calculate Fisher's exact test statistic between two feature files.\n\
  \nThis tool performs Fisher's exact test to assess the statistical significance\n\
  of overlaps between genomic intervals in two files. It calculates the probability\n\
  of observing the given overlap pattern by chance, providing a p-value for \nstatistical\
  \ inference.\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"
- "intervals"
- "fisher"
- "statistics"
- "overlap"
- "significance"
- "test"
license: "MIT"
references:
  doi:
  - "10.1093/bioinformatics/btq033"
links:
  repository: "https://github.com/arq5x/bedtools2"
  homepage: "https://bedtools.readthedocs.io/"
  documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/fisher.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_fisher/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_fisher"
  executable: "target/executable/bedtools/bedtools_fisher/bedtools_fisher"
  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"
