name: "bedtools_merge"
namespace: "bedtools"
version: "add_sgdemux"
authors:
- name: "Theodoro Gasperin Terra Camargo"
  roles:
  - "author"
  - "maintainer"
  info:
    links:
      email: "theodorogtc@gmail.com"
      github: "tgaspe"
      linkedin: "theodoro-gasperin-terra-camargo"
    organizations:
    - name: "Data Intuitive"
      href: "https://www.data-intuitive.com"
      role: "Bioinformatician"
argument_groups:
- name: "Inputs"
  arguments:
  - type: "file"
    name: "--input"
    alternatives:
    - "-i"
    description: "Input file (BED/GFF/VCF) to be merged."
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    description: "Output merged file BED to be written."
    info: null
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Options"
  arguments:
  - type: "boolean_true"
    name: "--strand"
    alternatives:
    - "-s"
    description: "Force strandedness. That is, only merge features\nthat are on the\
      \ same strand.\n- By default, merging is done without respect to strand.\n"
    info: null
    direction: "input"
  - type: "string"
    name: "--specific_strand"
    alternatives:
    - "-S"
    description: "Force merge for one specific strand only.\nFollow with + or - to\
      \ force merge from only\nthe forward or reverse strand, respectively.\n- By\
      \ default, merging is done without respect to strand.\n"
    info: null
    required: false
    choices:
    - "+"
    - "-"
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--distance"
    alternatives:
    - "-d"
    description: "Maximum distance between features allowed for features\nto be merged.\n\
      - Def. 0. That is, overlapping & book-ended features are merged.\n- (INTEGER)\n\
      - Note: negative values enforce the number of b.p. required for overlap.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--columns"
    alternatives:
    - "-c"
    description: "Specify columns from the B file to map onto intervals in A.\nDefault:\
      \ 5.\nMultiple columns can be specified in a comma-delimited list.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--operation"
    alternatives:
    - "-o"
    description: "Specify the operation that should be applied to -c.\nValid operations:\n\
      \    sum, min, max, absmin, absmax,\n    mean, median, mode, antimode\n    stdev,\
      \ sstdev\n    collapse (i.e., print a delimited list (duplicates allowed)),\
      \ \n    distinct (i.e., print a delimited list (NO duplicates allowed)), \n\
      \    distinct_sort_num (as distinct, sorted numerically, ascending),\n    distinct_sort_num_desc\
      \ (as distinct, sorted numerically, desscending),\n    distinct_only (delimited\
      \ list of only unique values),\n    count\n    count_distinct (i.e., a count\
      \ of the unique values in the column), \n    first (i.e., just the first value\
      \ in the column), \n    last (i.e., just the last value in the column), \nDefault:\
      \ sum\nMultiple operations can be specified in a comma-delimited list.\n\nIf\
      \ there is only column, but multiple operations, all operations will be\napplied\
      \ on that column. Likewise, if there is only one operation, but\nmultiple columns,\
      \ that operation will be applied to all columns.\nOtherwise, the number of columns\
      \ must match the the number of operations,\nand will be applied in respective\
      \ order.\nE.g., \"-c 5,4,6 -o sum,mean,count\" will give the sum of column 5,\n\
      the mean of column 4, and the count of column 6.\nThe order of output columns\
      \ will match the ordering given in the command.\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--delimiter"
    alternatives:
    - "-delim"
    description: "Specify a custom delimiter for the collapse operations.\n"
    info: null
    example:
    - "|"
    default:
    - ","
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--precision"
    alternatives:
    - "-prec"
    description: "Sets the decimal precision for output (Default: 5).\n"
    info: null
    required: false
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "boolean_true"
    name: "--bed"
    description: "If using BAM input, write output as BED.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--header"
    description: "Print the header from the A file prior to results.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--no_buffer"
    alternatives:
    - "-nobuf"
    description: "Disable buffered output. Using this option will cause each line\n\
      of output to be printed as it is generated, rather than saved\nin a buffer.\
      \ This will make printing large output files \nnoticeably slower, but can be\
      \ useful in conjunction with\nother software tools and scripts that need to\
      \ process one\nline of bedtools output at a time.\n"
    info: null
    direction: "input"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Merges overlapping BED/GFF/VCF entries into a single interval.\n"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
- type: "file"
  path: "test_data"
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
license: "MIT"
references:
  doi:
  - "10.1093/bioinformatics/btq033"
links:
  repository: "https://github.com/arq5x/bedtools2"
  homepage: "https://bedtools.readthedocs.io/en/latest/#"
  documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/merge.html"
  issue_tracker: "https://github.com/arq5x/bedtools2/issues"
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: "debian:stable-slim"
  target_registry: "images.viash-hub.com"
  target_tag: "add_sgdemux"
  namespace_separator: "/"
  setup:
  - type: "apt"
    packages:
    - "bedtools"
    - "procps"
    interactive: false
  - type: "docker"
    run:
    - "echo \"bedtools: \\\"$(bedtools --version | sed -n 's/^bedtools //p')\\\"\"\
      \ > /var/software_versions.txt\n"
  entrypoint: []
  cmd: null
- type: "native"
  id: "native"
build_info:
  config: "src/bedtools/bedtools_merge/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_merge"
  executable: "target/executable/bedtools/bedtools_merge/bedtools_merge"
  viash_version: "0.9.0"
  git_commit: "402ad6a813c0d0b141bbf8f9a3aab9c270a74812"
  git_remote: "https://x-access-token:ghs_VWGBwCOTHxXRJ07uVE94xFn8UJ2FmS0FLhmc@github.com/viash-hub/biobox"
  git_tag: "v0.2.0-27-g402ad6a"
package_config:
  name: "biobox"
  version: "add_sgdemux"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0"
  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 := 'add_sgdemux'"
  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"
