معرفی شرکت ها

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

توضیحات

Instrument for forming Galaxy XML and CWL tool descriptions from argparse arguments

ویژگی	مقدار
سیستم عامل	-
نام فایل	argparse2tool-0.4.9
نام	argparse2tool
نسخه کتابخانه	0.4.9
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Helena Rasche, Anton Khodak
ایمیل نویسنده	hxr@hx42.org
آدرس صفحه اصلی	https://github.com/hexylena/argparse2tool
آدرس اینترنتی	https://pypi.org/project/argparse2tool/
مجوز	-

argparse2tool ============= |PyPI| |Build Status| This project aims to provide a drop-in replacement for argparse which allows generating Galaxy XML and CWL Tools. It is quite literally a drop-in replacement. You (or the upstream tool author) can use argparse completely as normal .. code:: python import argparse When this package is installed and PYTHONPATH=$(argparse2tool) is set the dropin replacement of argparse is used ahead of the system argparse, ``argparse2tool`` will capture all argparse function calls, and process them specially. This information captured in this process is used to produce `Galaxy Tool XML <https://github.com/hexylena/galaxyxml>`__ when it's requested with the ``--generate_galaxy_xml`` flag, or `CWL Tools <http://www.commonwl.org/v1.0/CommandLineTool.html>`__ when requested with the ``--generate_cwl_tool`` flag. For our `example python script <./examples/example.py>`__ you can see the generated `Galaxy XML <./examples/example.xml>`__ and `CWL Tools <./examples/example.cwl>`__. Running ------- To generate XML or CWL, run your tool with the appropriate command line flag .. code:: console $ PYTHONPATH=$(argparse2tool) <tool command> --generate_galaxy_xml <other options> > tool.xml $ PYTHONPATH=$(argparse2tool) <tool command> --generate_cwl_tool <other options> > tool.cwl The project includes a sample ``example.py`` file which uses as many argparse features as possible. CWL and Galaxy XML support different portions feature sets which will be visible in the generated outputs. .. code:: console $ PYTHONPATH=$(argparse2tool) python example.py --generate_galaxy_xml $ PYTHONPATH=$(argparse2tool) python example.py --generate_cwl_tool CWL Specific Functionality ~~~~~~~~~~~~~~~~~~~~~~~~~~ Example for `CNVkit <https://github.com/etal/cnvkit>`__ toolkit .. code:: console $ cnvkit.py batch --generate_cwl_tool -d ~/cnvkit-tools/ --generate_outputs If there are subcommands in the provided command, all possible tools will be generated, for instance, for CNVkit .. code:: console $ cnvkit.py --generate_cwl_tool will produce CWL tool descriptions for ``cnvkit.py batch``, ``cnvkit.py access``, ``cnvkit.py export bed``, ``cnvkit.py export cdt`` and all other subcommands. Other options (which work only with ``--generate_cwl_tool`` provided, except for help message) are: - ``-o FILENAME``, ``--output_section FILENAME``: File with manually filled output section which is put to a formed CWL tool. ``argparse2tool`` is not very good at generating outputs, it recognizes output files only if they have type ``argparse.FileType('w')``, so output section is often blank and should be filled manually. - ``-go``, ``--generate_outputs``: flag for generating outputs not only from arguments that are instances of ``argparse.FileType('w')``, but also from every argument which contains ``output`` keyword in its name. For instance, argument ``--output-file`` with no type will also be placed to output section. However, '--output-directory' argument will also be treated like File, so generated tools must be checked carefully if when this option is selected. - ``-b``, ``basecommand``: command which appears in ``basecommand`` field in a resulting tool. It is handy to use this option when you run tool with shebang, but want ``python`` to be in ``basecommand`` field and the file amidst arguments. Example: ``$ .search.py --generate_cwl_tool -b python``. Basecommand of the formed tool will be ``['python']``, and ``search`` will be a positional argument on position 0. - ``-d``, ``--directory``: directory for storing tool descriptions. - ``--help_arg2cwl``: prints this help message. How it works ------------ Internally, ``argparse2tool``, masquerading as ``argparse`` attempts to find and import the **real** argparse. It then stores a reference to the code module for the system argparse, and presents the user with all of the functions that stdlib's argparse provides. Every function call is passed through the system argparse. However, argparse2tool captures the details of those calls and when Tool XML or CWL is requested, it builds up the tool definition and prints it out to standard output. Examples -------- You can see the ``example.py`` file for an example with numerous types of arguments and options that you might see in real tools. Accordingly there is an ``example.xml`` file with the output. It doesn't work!! ----------------- If you are not able to use the ``--generate_galaxy_xml``/``--generate_cwl_tool`` flags after installing, it is probably because of module load order. ``argparse2tool`` must precede ``argparse`` in the path. To easily correct this, run the tool ``argparse2tool`` which is installed as part of this package. Correctly functioning paths will produce the following: .. code:: console $ argparse2tool PATH_TO_THE_DROPINS while incorrectly ordered paths will produce a helpful error message: .. code:: console $ argparse2tool no dropins dir... This is intended to be used inline: .. code:: console user@host:$ PYTHONPATH=$(argparse2tool) python my_script.py --generate_galaxy_xml Limitations ----------- This code doesn't cover the entirety of the ``argparse`` API yet, and there are some bugs to work out on the XML generation side: - argparse - groups not supported (in galaxy, everything should still work in argparse) - some features like templating of the version string (please submit bugs) - galaxyxml - bugs in conditionals/whens (probably) - argparse2tool Galaxy XML Output - support declaring output files in an ``argparse``-esque manner - argparse2tool CWL Output - Some of argparse features can not be ported to CWL. 1. ``nargs=N``. Number of arguments can not be specified in CWL (yet). 2. ``const`` argument of ``add_argument()``. All constants must be specified in job files. 3. Custom types and custom actions are not supported. 4. Argument groups don't work in CWL as arguments are sorted with a `special algorithm <http://www.commonwl.org/draft-3/CommandLineTool.html#Input_binding>`__ 5. Mutual exclusion is not supported. License ------- Apache License, v2 .. |PyPI| image:: https://img.shields.io/pypi/v/argparse2tool.svg :target: https://pypi.python.org/pypi/argparse2tool .. |Build Status| image:: https://travis-ci.org/hexylena/argparse2tool.svg?branch=master :target: https://travis-ci.org/hexylena/argparse2tool

نیازمندی

مقدار	نام
==0.4.6	galaxyxml
-	jinja2

نحوه نصب

نصب پکیج whl argparse2tool-0.4.9:

pip install argparse2tool-0.4.9.whl

نصب پکیج tar.gz argparse2tool-0.4.9:

pip install argparse2tool-0.4.9.tar.gz