acclimatise 1.2.0

Description:

acclimatise 1.2.0

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}
>>>
}