planemo.training package¶
Submodules¶
planemo.training.tool_input module¶
Module contains code for the ToolInput class, dealing with the description of tool in workflow and XML.
-
class
planemo.training.tool_input.
ToolInput
(tool_inp_desc, wf_param_values, wf_steps, level, should_be_there=False, force_default=False)[source]¶ Bases:
object
Class to describe a tool input / parameter and its value from a workflow.
-
get_formatted_conditional_desc
()[source]¶ Format the description (label and value) for parameters in a conditional.
-
get_formatted_desc
()[source]¶ Get the formatted description (ready for hands-on tutorial) of the parameter.
-
get_formatted_other_param_desc
()[source]¶ Get value of a ‘simple’ parameter if different from the default value, None otherwise.
-
get_formatted_repeat_desc
()[source]¶ Format the description (label and value) for parameters in a repeat.
-
planemo.training.topic module¶
Module contains code for the Topic class, dealing with the creation of a training topic.
-
class
planemo.training.topic.
Topic
(name='new_topic', target='use', title='The new topic', summary='Summary', parent_dir='topics')[source]¶ Bases:
object
Class to describe a training topic.
planemo.training.tutorial module¶
Module contains code for the Tutorial class, dealing with the creation of a training tutorial.
-
class
planemo.training.tutorial.
Tutorial
(training, topic, name='new_tuto', title='The new tutorial', zenodo_link='')[source]¶ Bases:
object
Class to describe a training tutorial.
-
create_hands_on_tutorial
(ctx)[source]¶ Create tutorial structure from the workflow file (if it is provided).
-
get_files_from_zenodo
()[source]¶ Extract a list of URLs and dictionary describing the files from the JSON output of the Zenodo API.
-
init_from_existing_tutorial
(tuto_name)[source]¶ Init a tutorial instance from an existing tutorial (data library and tutorial.md).
-
-
planemo.training.tutorial.
format_wf_steps
(wf, gi)[source]¶ Get a string with the hands-on boxes describing the different steps of the worklow.
-
planemo.training.tutorial.
get_galaxy_datatype
(z_ext, datatype_fp)[source]¶ Get the Galaxy datatype corresponding to a Zenodo file type.
-
planemo.training.tutorial.
get_hands_on_boxes_from_local_galaxy
(kwds, wf_filepath, ctx)[source]¶ Server local Galaxy and get the workflow dictionary.
-
planemo.training.tutorial.
get_hands_on_boxes_from_running_galaxy
(wf_id, galaxy_url, galaxy_api_key)[source]¶ Get the workflow dictionary from a running Galaxy instance with the workflow installed on it.
-
planemo.training.tutorial.
get_wf_inputs
(step_inp)[source]¶ Get the inputs from a workflow step and format them into a hierarchical dictionary.
planemo.training.utils module¶
Module contains code for the Requirement, Reference and some general functions for training.
-
class
planemo.training.utils.
Requirement
(req_type='internal', topic_name='introduction', title=None, tutorials=None, link=None)[source]¶ Bases:
object
Class to describe a training requirement.