Skip to main content

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

Project description

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}
  >>>
}

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for acclimatise, version 1.2.0
Filename, size File type Python version Upload date Hashes
Filename, size acclimatise-1.2.0-py3-none-any.whl (67.9 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size acclimatise-1.2.0.tar.gz (44.3 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page