https://github.com/aCLImatise/CliHelpParser

Reads the output from CLI help commands, and generates machine readable schemas (CWL etc)
https://github.com/aCLImatise/CliHelpParser

bioinformatics cli cwl parser pipeline wdl workflow

Last synced: 2 months ago
JSON representation

Reads the output from CLI help commands, and generates machine readable schemas (CWL etc)

• Host: GitHub
• URL: https://github.com/aCLImatise/CliHelpParser
• Owner: aCLImatise
• License: gpl-3.0
• Created: 2019-02-25T05:27:43.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2021-02-14T15:00:22.000Z (almost 4 years ago)
• Last Synced: 2024-10-04T08:36:26.228Z (3 months ago)
• Topics: bioinformatics, cli, cwl, parser, pipeline, wdl, workflow
• Language: Python
• Homepage: https://aclimatise.github.io/CliHelpParser/
• Size: 1.16 MB
• Stars: 14
• Watchers: 3
• Forks: 5
• Open Issues: 22
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

Awesome Lists containing this project

README

        
aCLImatise

***********

|DOI|

.. |DOI| image:: https://zenodo.org/badge/DOI/10.1093/bioinformatics/btaa1033.svg

   :target: https://doi.org/10.1093/bioinformatics/btaa1033

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

`_.

======================================================================

aCLImatise 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 aCLImatise supports both `CWL `_ and

`WDL `_ outputs, but other formats will be considered in the future, especially pull

requests to support them.

Please also refer to `The aCLImatise Base Camp `_, which is a database of pre-computed tool definitions

generated by the aCLImatise parser. Most bioinformatics tools have a tool definition already generated in the Base Camp,

so you may not need to run aCLImatise directly.

aCLImatise is now published in the journal *Bioinformatics*. You can read the application note here: https://doi.org/10.1093/bioinformatics/btaa1033.

To cite aCLImatise, please use the citation generator provided by the journal.

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: 

   Full documentation at: 

   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``:

.. 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}

      >>>

    }