name: "bedtools_tag"
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"
    alternatives:
    - "-i"
    description: "Input BAM file to annotate with tags.\n\n**Format:** BAM file with\
      \ aligned sequencing reads\n**Content:** Alignments that will be tagged based\
      \ on overlaps\n**Requirements:** Must be a valid BAM file (indexed .bai file\
      \ recommended)\n**Usage:** Each alignment overlapping with annotation files\
      \ will receive tags\n**Output:** Tagged BAM file with additional tag fields\n"
    info: null
    example:
    - "alignments.bam"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "file"
    name: "--files"
    description: "BED/GFF/VCF annotation files for tagging overlapping alignments.\n\
      \n**Format:** BED, GFF, or VCF files with genomic intervals\n**Content:** Genomic\
      \ features used for alignment annotation\n**Usage:** Alignments overlapping\
      \ these intervals receive tags\n**Multiple files:** Each file can have its own\
      \ label for distinction\n**Requirements:** Files should have consistent chromosome\
      \ naming with BAM\n"
    info: null
    example:
    - "genes.bed"
    - "enhancers.bed"
    - "repeats.bed"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: true
    multiple_sep: ";"
  - type: "string"
    name: "--labels"
    description: "Labels corresponding to each annotation file.\n\n**Format:** String\
      \ labels for each annotation file\n**Usage:** Must provide one label per annotation\
      \ file in --files\n**Content:** These labels will be used as tag values in the\
      \ BAM output\n**Order:** Must match the order of files in --files parameter\n\
      **Applications:** Distinguish overlaps from different annotation sources\n**Note:**\
      \ Required unless --use_names, --use_scores, or --use_intervals is specified\n"
    info: null
    example:
    - "GENE"
    - "ENHANCER"
    - "REPEAT"
    required: false
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    description: "Output BAM file with tagged alignments.\n\n**Format:** BAM file\
      \ with original alignments plus overlap tags\n**Content:** All original alignment\
      \ data plus custom tags for overlaps\n**Tags:** Alignments overlapping annotation\
      \ files receive additional tag fields\n**Preservation:** Non-overlapping alignments\
      \ remain unchanged\n**Indexing:** Output can be indexed like any standard BAM\
      \ file\n"
    info: null
    example:
    - "tagged_alignments.bam"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Overlap Options"
  arguments:
  - type: "double"
    name: "--min_overlap"
    alternatives:
    - "-f"
    description: "Minimum overlap required as a fraction of the alignment.\n\n**Default:**\
      \ 1E-9 (essentially 1 base pair)\n**Range:** 0.0 to 1.0\n**Usage:** Alignment\
      \ must overlap at least this fraction of its length\n**Example:** 0.5 requires\
      \ alignment to overlap 50% of its length with feature\n**Applications:** Filter\
      \ spurious overlaps, require substantial overlap\n"
    info: null
    example:
    - 0.1
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Strand Options"
  arguments:
  - type: "boolean_true"
    name: "--same_strand"
    alternatives:
    - "-s"
    description: "Require overlaps on the same strand.\n\n**Usage:** Only tag alignments\
      \ that overlap features on the same strand\n**Applications:** Strand-specific\
      \ RNA-seq analysis, sense transcript tagging\n**Default:** false (overlaps reported\
      \ without respect to strand)\n**Interaction:** Mutually exclusive with --opposite_strand\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--opposite_strand"
    alternatives:
    - "-S"
    description: "Require overlaps on the opposite strand.\n\n**Usage:** Only tag\
      \ alignments that overlap features on the opposite strand\n**Applications:**\
      \ Antisense transcript detection, strand-specific filtering\n**Default:** false\
      \ (overlaps reported without respect to strand)\n**Interaction:** Mutually exclusive\
      \ with --same_strand\n"
    info: null
    direction: "input"
- name: "Tag Options"
  arguments:
  - type: "string"
    name: "--tag_name"
    alternatives:
    - "-tag"
    description: "Specify the BAM tag name to use for annotations.\n\n**Default:**\
      \ \"YB\" \n**Format:** Two-character string (standard BAM tag format)\n**Usage:**\
      \ Custom tag name for storing overlap information\n**Examples:** \"YK\", \"\
      ZZ\", \"XG\"\n**Standards:** Follow BAM tag naming conventions\n"
    info: null
    example:
    - "YK"
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--use_names"
    alternatives:
    - "-names"
    description: "Use the name field from annotation files to populate tags.\n\n**Usage:**\
      \ Instead of labels, use the name column from BED/GFF files\n**Applications:**\
      \ Gene name tagging, feature-specific annotation\n**Requirements:** Annotation\
      \ files must have name fields (4th column in BED)\n**Default:** false (uses\
      \ --labels values instead)\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--use_scores"
    alternatives:
    - "-scores"
    description: "Use the score field from annotation files to populate tags.\n\n\
      **Usage:** Instead of labels, use the score column from annotation files\n**Applications:**\
      \ Confidence scoring, quantitative tagging\n**Requirements:** Annotation files\
      \ must have score fields (5th column in BED)\n**Default:** false (uses --labels\
      \ values instead)\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--use_intervals"
    alternatives:
    - "-intervals"
    description: "Use full interval information to populate tags.\n\n**Content:**\
      \ Include interval coordinates, name, score, and strand in tags\n**Format:**\
      \ Full genomic interval description as tag value\n**Applications:** Detailed\
      \ annotation tracking, interval provenance\n**Requirements:** Still requires\
      \ --labels to identify source files\n**Default:** false (uses --labels values\
      \ instead)\n"
    info: null
    direction: "input"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Annotate BAM alignments with tags based on overlaps with genomic intervals.\n\
  \nbedtools tag reads alignments from a BAM file and annotates them with custom tags\
  \ \nbased on their overlap with intervals from one or more BED/GFF/VCF files. Each\
  \ \nalignment that overlaps with an interval receives a tag in the BAM record, making\
  \ \nthis tool essential for marking reads that overlap with specific genomic features\
  \ \nlike genes, enhancers, or repetitive elements.\n\nThis tool is commonly used\
  \ for:\n- Tagging reads that overlap with specific genomic features\n- Annotating\
  \ alignments with gene names or functional regions\n- Marking reads for downstream\
  \ filtering based on overlap patterns\n- Quality control by identifying reads in\
  \ problematic regions\n- Single-cell RNA-seq analysis for feature assignment\n-\
  \ ChIP-seq analysis for peak annotation and read classification\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"
- "bam"
- "annotation"
- "tagging"
- "overlap"
- "alignment"
- "features"
license: "MIT"
references:
  doi:
  - "10.1093/bioinformatics/btq033"
links:
  repository: "https://github.com/arq5x/bedtools2"
  homepage: "https://bedtools.readthedocs.io/en/latest/content/tools/tag.html"
  documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/tag.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_tag/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_tag"
  executable: "target/executable/bedtools/bedtools_tag/bedtools_tag"
  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"
