Merge pull request #21 from illusional/origin-pr

Big PR

Author: mr-c

.gitignore

@@ -6,3 +6,6 @@ build/
 cwlgen.egg*
 dist/
 *.pyc
+.DS_Store
+.idea/
+.coverage

README.md

@@ -11,22 +11,69 @@ The library works for both Python 2.7.12+ and 3.6.0.
 
 ------------------------
 
-# Quick-start guide
 
-## Installation
+# Common Workflow Language
 
-You can install python-cwlgen using pip with the following command:
+[Common Workflow Language (CWL)](https://www.commonwl.org/v1.0/index.html) is a language to describe workflows. 
+The [user guide](http://www.commonwl.org/user_guide/01-introduction/index.html)
+ gives a gentle explanation of what its goals are, but broadly:
+ 
+ 1. Stop writing bash scripts for long complex jobs.
+ 2. Take pipelines anywhere (portability).
+ 3. Enforce reproducibility guidelines.
+ 
+This python repository is a python wrapper for _most_ of the classes (work in progress), 
+allowing you to build the structure of the workflow in Python and have this module generate and export CWL for you.
+
+**Nb:** This doesn't check the logic of Workflows or CommandLineTools for you.  
+[CWLTool](https://github.com/common-workflow-language/cwltool) has a `--validate` mode that you can use.
+
+## Quick-start guide
+
+You can install python-cwlgen through pip with the following command:
 
 ```bash
 pip install cwlgen
 ```
 
-## How it works ?
+### How it works?
+
+This repository contains a number of python classes that mirror the CWL specifications ([Workflow](https://www.commonwl.org/v1.0/Workflow.html)| 
+[CommandLineTool](https://www.commonwl.org/v1.0/CommandLineTool.html)). In essence, each class's initializer has all 
+of the properties it expects, which may be another object. The classes include the relevant docstrings to give you 
+context of classes and their properties.
+
+The `examples/` folder contains some simple examples, however in essence you simply initialize the class you're 
+trying to build. An initializer for a class has all of the properties it expects which may be another object.
+
 
-An example of usage is available in the `example/` folder of the repository (more details [here](http://python-cwlgen.readthedocs.io/en/latest/user_guide.html))
+_Creating a CommandLineTool_
+```python
+import cwlgen
+
+tool_object = cwlgen.CommandLineTool(tool_id="echo-tool", base_command="echo", label=None, doc=None,
+                 cwl_version="v1.0", stdin=None, stderr=None, stdout=None, path=None)
+tool_object.inputs.append(
+    cwlgen.CommandInputParameter("myParamId", param_type="string", label=None, secondary_files=None, param_format=None,
+                 streamable=None, doc=None, input_binding=None, default=None)
+)
+
+# to get the dictionary representation:
+dict_to_export = tool_object.get_dict()
+
+# to get the string representation (YAML)
+yaml_export = tool_object.export_string()
+
+# print to console
+tool_object.export()
+
+# print to file
+with open("echotool.cwl", "w") as f:
+    tool_object.export(f)
+```
 
 ## References
 
-CWL is developed by an informal, multi-vendor working group consisting of organizations and
-individuals aiming to enable scientists to share data analysis workflows.
-[The CWL project is on Github.](https://github.com/common-workflow-language/common-workflow-language)
+CWL is developed by an informal, multi-vendor working group consisting of organizations and individuals 
+aiming to enable scientists to share data analysis workflows. 
+The [CWL project is on Github](https://github.com/common-workflow-language/common-workflow-language).