Acclimatise

For the full documentation, refer to the Github Pages Website.

Acclimatise is a Python library and command-line utility for parsing the help output of a command-line tool and then outputting a description of the tool in a more structured format, for example a Common Workflow Language tool definition.

Currently Acclimatise supports both CWL and WDL outputs, but other formats will be considered in the future, especially pull requests to support them.

Example

Lets say you want to create a CWL workflow containing the common Unix wc (word count) utility. Running wc --help returns:

Usage: wc [OPTION]... [FILE]...
  or: wc [OPTION]... --files0-from=F
Print newline, word, and byte counts for each FILE, and a total line if
more than one FILE is specified.  A word is a non-zero-length sequence of
characters delimited by white space.

With no FILE, or when FILE is -, read standard input.

The options below may be used to select which counts are printed, always in
the following order: newline, word, character, byte, maximum line length.
  -c, --bytes            print the byte counts
  -m, --chars            print the character counts
  -l, --lines            print the newline counts
      --files0-from=F    read input from the files specified by
                           NUL-terminated names in file F;
                           If F is - then read names from standard input
  -L, --max-line-length  print the maximum display width
  -w, --words            print the word counts
      --help display this help and exit
      --version output version information and exit

GNU coreutils online help: <http://www.gnu.org/software/coreutils/>
Full documentation at: <http://www.gnu.org/software/coreutils/wc>
or available locally via: info '(coreutils) wc invocation'

If you run acclimatise explore wc, which means “parse the wc command and all subcommands”, you’ll end up with the following files in your current directory:

wc.cwl
wc.wdl
wc.yml

These are representations of the command wc in 3 different formats. If you look at wc.wdl, you’ll see that it contains a WDL-compatible tool definition for wc:

version 1.0
task Wc {
  input {
    Boolean bytes
    Boolean chars
    Boolean lines
    String files__from
    Boolean max_line_length
    Boolean words
  }
  command <<<
    wc \
      ~{true="--bytes" false="" bytes} \
      ~{true="--chars" false="" chars} \
      ~{true="--lines" false="" lines} \
      ~{if defined(files__from) then ("--files0-from " +  '"' + files__from + '"') else ""} \
      ~{true="--max-line-length" false="" max_line_length} \
      ~{true="--words" false="" words}
  >>>
}

Release files for acclimatise 1.2.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for acclimatise 1.2.0
File	Size	Uploaded
acclimatise-1.2.0.tar.gz	44.3 kB	Sep 12, 2020	Details

Built distribution (wheel)

Table of built distributions (wheels) for acclimatise 1.2.0
File	Interpreter	ABI	Platform	Reset
acclimatise-1.2.0-py3-none-any.whl 67.9 kB Sep 12, 2020	Python 3	none	any	Details

Total release size: 112.2 kB

Release files / acclimatise-1.2.0.tar.gz

Download URL	acclimatise-1.2.0.tar.gz
Size	44.3 kB
Tags	Source
SHA-256 checksum How to use checksums	`178684918b3b12fca929e4eeee5534cc8347dcb7462f4931ffb8bc47e1a5fe6d`
BLAKE2b-256 checksum How to use checksums	`abb0a1acde0c2e347bea4d7adb980a9e8a3f6a83b8883cca16f0646f2db22d39`
Upload date	Sep 12, 2020
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/3.2.0 pkginfo/1.5.0.1 requests/2.24.0 setuptools/50.3.0 requests-toolbelt/0.9.1 tqdm/4.48.2 CPython/3.8.5`

Release files / acclimatise-1.2.0-py3-none-any.whl

Download URL	acclimatise-1.2.0-py3-none-any.whl
Size	67.9 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`658cfade26faa2227caba6bf8b1fe3824e88568ce8969bf049cb7c6693f4a8c8`
BLAKE2b-256 checksum How to use checksums	`0673ecbdae2bdcbbf5eaa0158681c789d8cca0479b125c808eabed4c02195757`
Upload date	Sep 12, 2020
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/3.2.0 pkginfo/1.5.0.1 requests/2.24.0 setuptools/50.3.0 requests-toolbelt/0.9.1 tqdm/4.48.2 CPython/3.8.5`