Concatenate¶

cat · 0 contributors · 1 version

The cat utility reads files sequentially, writing them to the standard output. The file operands are processed in command-line order. If file is a single dash (`-’) or absent,cat reads from the standard input. If file is a UNIX domain socket, cat connects to it and then reads it until EOF. This complements the UNIX domain binding capability available in inetd(8).

Quickstart¶

from janis_unix.tools.cat import Cat

wf = WorkflowBuilder("myworkflow")

wf.step(
    "cat_step",
    Cat(

    )
)
wf.output("out", source=cat_step.out)

OR

Install Janis
Ensure Janis is configured to work with Docker or Singularity.
Ensure all reference files are available:

Note

More information about these inputs are available below.

Generate user input files for cat:

# user inputs
janis inputs cat > inputs.yaml

inputs.yaml

{}

Run cat with:

janis run [...run options] \
    --inputs inputs.yaml \
    cat

Information¶

ID:	`cat`
URL:	No URL to the documentation was provided
Versions:	v1.0.0
Container:	ubuntu@sha256:1d7b639619bdca2d008eca2d5293e3c43ff84cbee597ff76de3b7a7de3e84956
Authors:
Citations:	None
Created:	None
Updated:	2019-07-26 00:00:00

Outputs¶

name	type	documentation
out	stdout<File>

Additional configuration (inputs)¶

name	type	prefix	position	documentation
file	Optional<File>
files	Optional<Array<File>>		1
number_output	Optional<Boolean>	-n		Number the output lines, starting at 1.
number_non_blank	Optional<Boolean>	-b		Number the non-blank output lines, starting at 1.
disable_output_buffer	Optional<Boolean>	-u		Disable output buffering.
squeeze	Optional<Boolean>	-s		Squeeze multiple adjacent empty lines, causing the output to be single spaced.
display_nonprint_and_eol_chars	Optional<Boolean>	-e		Display non-printing characters (see the -v option), and display a dollar sign (`$’) at the end of each line.
display_nonprint_and_tab_chars	Optional<Boolean>	-t		Display non-printing characters (see the -v option), and display tab characters as `^I’.
display_nonprint_chars	Optional<Boolean>	-v		Display non-printing characters so they are visible. Control characters print as `^X’ for control-X; the delete character (octal 0177) prints as `^?’. Non-ASCII characters (with the high bit set) are printed as `M-’ (for meta) followed by the character for the low 7 bits.

Workflow Description Language¶

version development

task cat {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File? file
    Array[File]? files
    Boolean? number_output
    Boolean? number_non_blank
    Boolean? disable_output_buffer
    Boolean? squeeze
    Boolean? display_nonprint_and_eol_chars
    Boolean? display_nonprint_and_tab_chars
    Boolean? display_nonprint_chars
  }
  command <<<
    set -e
    cat \
      ~{if (defined(number_output) && select_first([number_output])) then "-n" else ""} \
      ~{if (defined(number_non_blank) && select_first([number_non_blank])) then "-b" else ""} \
      ~{if (defined(disable_output_buffer) && select_first([disable_output_buffer])) then "-u" else ""} \
      ~{if (defined(squeeze) && select_first([squeeze])) then "-s" else ""} \
      ~{if (defined(display_nonprint_and_eol_chars) && select_first([display_nonprint_and_eol_chars])) then "-e" else ""} \
      ~{if (defined(display_nonprint_and_tab_chars) && select_first([display_nonprint_and_tab_chars])) then "-t" else ""} \
      ~{if (defined(display_nonprint_chars) && select_first([display_nonprint_chars])) then "-v" else ""} \
      ~{if (defined(files) && length(select_first([files])) > 0) then "'" + sep("' '", select_first([files])) + "'" else ""}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "ubuntu@sha256:1d7b639619bdca2d008eca2d5293e3c43ff84cbee597ff76de3b7a7de3e84956"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    File out = stdout()
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Concatenate
doc: |-
  The cat utility reads files sequentially, writing them to the standard output. The file operands are processed in command-line order. If file is a single dash (`-') or absent,cat reads from the standard input. If file is a UNIX domain socket, cat connects to it and then reads it until EOF. This complements the UNIX domain binding capability available in inetd(8).

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: ubuntu@sha256:1d7b639619bdca2d008eca2d5293e3c43ff84cbee597ff76de3b7a7de3e84956

inputs:
- id: file
  label: file
  type:
  - File
  - 'null'
- id: files
  label: files
  type:
  - type: array
    items: File
  - 'null'
  inputBinding:
    position: 1
- id: number_output
  label: number_output
  doc: Number the output lines, starting at 1.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -n
- id: number_non_blank
  label: number_non_blank
  doc: Number the non-blank output lines, starting at 1.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -b
- id: disable_output_buffer
  label: disable_output_buffer
  doc: Disable output buffering.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -u
- id: squeeze
  label: squeeze
  doc: Squeeze multiple adjacent empty lines, causing the output to be single spaced.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -s
- id: display_nonprint_and_eol_chars
  label: display_nonprint_and_eol_chars
  doc: |-
    Display non-printing characters (see the -v option), and display a dollar sign (`$') at the end of each line.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -e
- id: display_nonprint_and_tab_chars
  label: display_nonprint_and_tab_chars
  doc: |-
    Display non-printing characters (see the -v option), and display tab characters as `^I'.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -t
- id: display_nonprint_chars
  label: display_nonprint_chars
  doc: |-
    Display non-printing characters so they are visible.  Control characters print as `^X' for control-X; the delete character (octal 0177) prints as `^?'.  Non-ASCII characters (with the high bit set) are printed as `M-' (for meta) followed by the character for the low 7 bits.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -v

outputs:
- id: out
  label: out
  type: stdout
stdout: _stdout
stderr: _stderr

baseCommand: cat
arguments: []

hints:
- class: ToolTimeLimit
  timelimit: |-
    $([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: cat