biobox/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml

name: "bedtools_groupby"
namespace: "bedtools"
version: "main"
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: "The input BED file to be used.\n"
    info: null
    example:
    - "input_a.bed"
    must_exist: true
    create_parent: true
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Outputs"
  arguments:
  - type: "file"
    name: "--output"
    description: "The output groupby BED file. \n"
    info: null
    example:
    - "output.bed"
    must_exist: true
    create_parent: true
    required: true
    direction: "output"
    multiple: false
    multiple_sep: ";"
- name: "Options"
  arguments:
  - type: "string"
    name: "--groupby"
    alternatives:
    - "-g"
    - "-grp"
    description: "Specify the columns (1-based) for the grouping.\nThe columns must\
      \ be comma separated.\n- Default: 1,2,3  \n"
    info: null
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "integer"
    name: "--column"
    alternatives:
    - "-c"
    - "-opCols"
    description: "Specify the column (1-based) that should be summarized.\n"
    info: null
    required: true
    direction: "input"
    multiple: false
    multiple_sep: ";"
  - type: "string"
    name: "--operation"
    alternatives:
    - "-o"
    - "-ops"
    description: "Specify the operation that should be applied to opCol.\nValid operations:\n\
      \    sum, count, count_distinct, min, max,\n    mean, median, mode, antimode,\n\
      \    stdev, sstdev (sample standard dev.),\n    collapse (i.e., print a comma\
      \ separated list (duplicates allowed)), \n    distinct (i.e., print a comma\
      \ separated list (NO duplicates allowed)), \n    distinct_sort_num (as distinct,\
      \ but sorted numerically, ascending), \n    distinct_sort_num_desc (as distinct,\
      \ but sorted numerically, descending), \n    concat   (i.e., merge values into\
      \ a single, non-delimited string), \n    freqdesc (i.e., print desc. list of\
      \ values:freq)\n    freqasc (i.e., print asc. list of values:freq)\n    first\
      \ (i.e., print first value)\n    last (i.e., print last value)\n\nDefault value:\
      \ sum   \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,\nthe 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: "boolean_true"
    name: "--full"
    description: "Print all columns from input file. The first line in the group is\
      \ used.\nDefault: print only grouped columns.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--inheader"
    description: "Input file has a header line - the first line will be ignored.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--outheader"
    description: "Print header line in the output, detailing the column names. \n\
      If the input file has headers (-inheader), the output file\nwill use the input's\
      \ column names.\nIf the input file has no headers, the output file\nwill use\
      \ \"col_1\", \"col_2\", etc. as the column names.\n"
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--header"
    description: "same as '-inheader -outheader'."
    info: null
    direction: "input"
  - type: "boolean_true"
    name: "--ignorecase"
    description: "Group values regardless of upper/lower case.\n"
    info: null
    direction: "input"
  - type: "integer"
    name: "--precision"
    alternatives:
    - "-prec"
    description: "Sets the decimal precision for output. \n"
    info: null
    default:
    - 5
    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: ";"
resources:
- type: "bash_script"
  path: "script.sh"
  is_executable: true
description: "Summarizes a dataset column based upon common column groupings. \nAkin\
  \ to the SQL \"group by\" command.\n"
test_resources:
- type: "bash_script"
  path: "test.sh"
  is_executable: true
info: null
status: "enabled"
requirements:
  commands:
  - "ps"
keywords:
- "groupby"
- "BED"
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/groupby.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: "main"
  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_groupby/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
  output: "target/executable/bedtools/bedtools_groupby"
  executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby"
  viash_version: "0.9.0"
  git_commit: "7f8bcc2b3e1ffaac9778b6acb42420b19660d1a1"
  git_remote: "https://x-access-token:ghs_aSDBedV4vU66pddFDN6d8UEy0ZQApn08RAsh@github.com/viash-hub/biobox"
  git_tag: "v0.2.0-3-g7f8bcc2"
package_config:
  name: "biobox"
  version: "main"
  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 := '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"