scriptcwl 0.6.0

# scriptcwl

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scriptcwl is a Python package for creating workflows in
[common workflow language](http://www.commonwl.org/). If you give it a number of CWL
`CommandLineTool`s, you can create a workflow by writing a Python script. This can
be done interactively using [Jupyter Notebooks](http://jupyter.org/). More information
about using scriptcwl can be found in the [documentation](http://scriptcwl.readthedocs.io/en/latest/).

```python
from scriptcwl import WorkflowGenerator

with WorkflowGenerator() as wf:
wf.load(steps_dir='/path_to_scriptcwl/scriptcwl/examples/')

num1 = wf.add_input(num1='int')
num2 = wf.add_input(num2='int')

answer1 = wf.add(x=num1, y=num2)
answer2 = wf.multiply(x=answer1, y=num2)

wf.add_outputs(final_answer=answer2)

wf.save('add_multiply_example_workflow.cwl')
```

This workflow has two integers as inputs (``num1`` and ``num2``), and first adds
these two numbers (``wf.add(x=num1, y=num2)``), and then multiplies the answer
with the second input (``num2``). The result of that processing step is the output
of the workflow. Finally, the workflow is saved to a file. The result looks like:

```
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
inputs:
num1: int
num2: int
outputs:
final_answer:
type: int
outputSource: multiply/answer
steps:
add:
run: add.cwl
in:
y: num2
x: num1
out:
- answer
multiply:
run: multiply.cwl
in:
y: num2
x: add/answer
out:
- answer
```

The Python and CWL files used in the example can be found in the [examples folder](https://github.com/NLeSC/scriptcwl/tree/master/scriptcwl/examples).

## Installation

Install using pip:

```
pip install scriptcwl
```

For development:

```
git clone git@github.com:NLeSC/scriptcwl.git
cd scriptcwl
git checkout develop
pip install -r requirements.txt
python setup.py develop
```

Run tests (including coverage) with:
```
python setup.py develop test
```

## Useful tools

To use scriptcwl for creating CWL workflows, you need CWL `CommandLineTool`s.
There are some software packages that help with generating those
for existing command line tools written in Python:

* [argparse2tool](https://github.com/erasche/argparse2tool#cwl-specific-functionality): Generate CWL CommandLineTool wrappers (and/or Galaxy tool descriptions) from Python programs that use argparse. Also supports the [click](http://click.pocoo.org) argument parser.
* [pypi2cwl](https://github.com/common-workflow-language/pypi2cwl): Automatically run argparse2cwl on any package in PyPi.
* [python-cwlgen](https://github.com/common-workflow-language/python-cwlgen): Generate CommandLineTool and DockerRequirement programmatically