acclimatise

Acclimatise

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For the full documentation, refer to the Github Pages Website <https://aclimatise.github.io/CliHelpParser/>_.

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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 <https://www.commonwl.org/v1.1/CommandLineTool.html>_.

Currently Acclimatise supports both CWL <https://www.commonwl.org/>_ and WDL <https://openwdl.org/>_ 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:

.. code-block::

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:

.. code-block:: text

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}
  >>>
}