name: "bedtools_map"
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: "First input file (intervals to annotate).\n\n**Format:** BED, GFF,\
      \ VCF file with genomic intervals\n**Requirement:** Must be sorted by chromosome,\
      \ then start position\n**Usage:** Each interval will be annotated with mapped\
      \ values from file B\n"
    info: null
    example:
    - "target_regions.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 (source of values to map).\n\n**Format:** BED,\
      \ GFF, VCF file with genomic intervals and data columns\n**Requirement:** Must\
      \ be sorted by chromosome, then start position\n**Usage:** Overlapping intervals\
      \ provide values for mapping operations\n"
    info: null
    example:
    - "data_intervals.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 mapped values appended to input A intervals.\n\n\
      **Format:** Same as input A with additional columns for mapped values\n**Content:**\
      \ Original columns from A plus computed statistical values\n**Order:** Follows\
      \ the order specified in column and operation parameters\n"
    info: null
    example:
    - "annotated_regions.bed"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Mapping Options"
  arguments:
  - type: "string"
    name: "--columns"
    alternatives:
    - "-c"
    description: "Columns from file B to use for mapping operations.\n\n**Default:**\
      \ 5 (fifth column, typically score column in BED)\n**Format:** Comma-delimited\
      \ list for multiple columns\n**Example:** \"5\" for score column, \"4,5\" for\
      \ name and score columns\n**Indexing:** 1-based column numbering\n"
    info: null
    example:
    - "5"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--operations"
    alternatives:
    - "-o"
    description: "Statistical operations to apply to specified columns.\n\n**Numeric\
      \ operations:** sum, min, max, absmin, absmax, mean, median, mode, antimode,\
      \ stdev, sstdev, count, count_distinct\n**List operations:** collapse, distinct,\
      \ distinct_sort_num, distinct_sort_num_desc, distinct_only\n**Position operations:**\
      \ first, last\n\n**Default:** sum\n**Format:** Comma-delimited list for multiple\
      \ operations\n**Pairing:** Operations applied to columns in respective order\n"
    info: null
    example:
    - "mean"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--delimiter"
    alternatives:
    - "-delim"
    description: "Custom delimiter for collapse operations.\n\n**Default:** \",\"\
      \ (comma)\n**Usage:** Only affects collapse, distinct, and related operations\n\
      **Example:** \"|\" for pipe-separated values, \";\" for semicolon-separated\n"
    info: null
    example:
    - "|"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--precision"
    alternatives:
    - "-prec"
    description: "Decimal precision for numerical output.\n\n**Default:** 5 decimal\
      \ places\n**Range:** 0-15 (reasonable range for floating point precision)\n\
      **Usage:** Controls rounding of computed statistical values\n"
    info: null
    example:
    - 3
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Overlap Options"
  arguments:
  - 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 by B\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 overlap A\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 consider\
      \ 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\
      \ consider overlaps on opposite strands\n**Default:** false (strand-independent)\n\
      **Note:** May have issues in some bedtools versions\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: "file"
    name: "--genome"
    alternatives:
    - "-g"
    description: "Genome file for consistent chromosome sorting.\n\n**Format:** Tab-delimited\
      \ file with chromosome name and size\n**Usage:** Only applies when used with\
      \ sorted data\n**Purpose:** Enforces consistent chromosome sort order\n"
    info: null
    example:
    - "genome.txt"
    must_exist: true
    create_parent: true
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - 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: "Apply statistical functions to columns from overlapping genomic intervals.\n\
  \nThis tool maps values from intervals in file B onto overlapping intervals in file\
  \ A\nby applying statistical operations (sum, mean, median, etc.). For each interval\
  \ in A,\nit finds all overlapping intervals in B and applies the specified function\
  \ to the \nspecified column(s). Useful for aggregating scores, computing statistics\
  \ over \ngenomic regions, or annotating intervals with quantitative data.\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"
- "map"
- "statistics"
- "aggregate"
- "annotate"
- "overlap"
- "scores"
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/map.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_map/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_map"
  executable: "target/executable/bedtools/bedtools_map/bedtools_map"
  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"
