aclimatise 3.0.1

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 aclimatise 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}
  >>>
}