cwltool.main
============

.. py:module:: cwltool.main

.. autoapi-nested-parse::

   Entry point for cwltool.



Attributes
----------

.. autoapisummary::

   cwltool.main.docker_exe
   cwltool.main.ProvOut


Classes
-------

.. autoapisummary::

   cwltool.main.ProvLogFormatter


Functions
---------

.. autoapisummary::

   cwltool.main.append_word_to_default_user_agent
   cwltool.main.generate_example_input
   cwltool.main.realize_input_schema
   cwltool.main.generate_input_template
   cwltool.main.load_job_order
   cwltool.main.init_job_order
   cwltool.main.make_relative
   cwltool.main.printdeps
   cwltool.main.prov_deps
   cwltool.main.find_deps
   cwltool.main.print_pack
   cwltool.main.supported_cwl_versions
   cwltool.main.setup_schema
   cwltool.main.setup_provenance
   cwltool.main.setup_loadingContext
   cwltool.main.make_template
   cwltool.main.inherit_reqshints
   cwltool.main.choose_target
   cwltool.main.choose_step
   cwltool.main.choose_process
   cwltool.main.check_working_directories
   cwltool.main.print_targets
   cwltool.main.main
   cwltool.main.find_default_container
   cwltool.main.windows_check
   cwltool.main.run


Module Contents
---------------

.. py:data:: docker_exe
   :type:  str

.. py:function:: append_word_to_default_user_agent(word)

   Append the specified word to the requests http user agent string if it's not already there.


.. py:function:: generate_example_input(inptype, default)

   Convert a single input schema into an example.


.. py:function:: realize_input_schema(input_types, schema_defs)

   Replace references to named typed with the actual types.


.. py:function:: generate_input_template(tool)

   Generate an example input object for the given CWL process.


.. py:function:: load_job_order(args, stdin, fetcher_constructor, overrides_list, tool_file_uri)

.. py:function:: init_job_order(job_order_object, args, process, loader, stdout, print_input_deps = False, relative_deps = 'primary', make_fs_access = StdFsAccess, input_basedir = '', secret_store = None, input_required = True, runtime_context = None)

.. py:function:: make_relative(base, obj)

   Relativize the location URI of a File or Directory object.


.. py:function:: printdeps(obj, document_loader, stdout, relative_deps, uri, basedir = None, nestdirs = True)

   Print a JSON representation of the dependencies of the CWL document.


.. py:function:: prov_deps(obj, document_loader, uri, basedir = None)

.. py:function:: find_deps(obj, document_loader, uri, basedir = None, nestdirs = True)

   Find the dependencies of the CWL document.


.. py:function:: print_pack(loadingContext, uri)

   Return a CWL serialization of the CWL document in JSON.


.. py:function:: supported_cwl_versions(enable_dev)

   Return a list of currently supported CWL versions.


.. py:function:: setup_schema(args, custom_schema_callback)

.. py:class:: ProvLogFormatter

   Bases: :py:obj:`logging.Formatter`

   .. autoapi-inheritance-diagram:: cwltool.main.ProvLogFormatter
      :parts: 1


   Enforce ISO8601 with both T and Z.


   .. py:method:: formatTime(record, datefmt = None)

      Override the default formatTime to include the timezone.



.. py:data:: ProvOut

.. py:function:: setup_provenance(args, runtimeContext, argsl = None)

.. py:function:: setup_loadingContext(loadingContext, runtimeContext, args)

   Prepare a LoadingContext from the given arguments.


.. py:function:: make_template(tool, target)

   Make a template CWL input object for the give Process.


.. py:function:: inherit_reqshints(tool, parent)

   Copy down requirements and hints from ancestors of a given process.


.. py:function:: choose_target(args, tool, loading_context)

   Walk the Workflow, extract the subset matches all the args.targets.


.. py:function:: choose_step(args, tool, loading_context)

   Walk the given Workflow and extract just args.single_step.


.. py:function:: choose_process(args, tool, loadingContext)

   Walk the given Workflow and extract just args.single_process.


.. py:function:: check_working_directories(runtimeContext)

   Make any needed working directories.


.. py:function:: print_targets(tool, stdout, loading_context, prefix = '')

   Recursively find targets for --subgraph and friends.


.. py:function:: main(argsl = None, args = None, job_order_object = None, stdin = sys.stdin, stdout = None, stderr = sys.stderr, versionfunc = versionstring, logger_handler = None, custom_schema_callback = None, executor = None, loadingContext = None, runtimeContext = None, input_required = True)

.. py:function:: find_default_container(builder, default_container = None, use_biocontainers = None, container_image_cache_path = None)

   Find a container.


.. py:function:: windows_check()

   See if we are running on MS Windows and warn about the lack of support.


.. py:function:: run(*args, **kwargs)

   Run cwltool.