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Exposing software inputs and outputs

We use IPython2CWL for a tool to convert IPython Jupyter Notebooks to CWL (Common Workflow Language) Command Line Tools by simply providing typing annotation.

Supported Types

The basic date types are:

  • Inputs:

    • CWLFilePathInput
    • CWLBooleanInput
    • CWLStringInput
    • CWLIntInput
    • CWLFloatInput

  • Outputs:

    • CWLFilePathOutput
    • CWLDumpableFile
    • CWLDumpableBinaryFile

In our example, we have 3 parameters a, b and c, an input file (which represents x) and a output file (which represents y)

a = 5
b = 4
c = 6
input_file = "./x.csv"
output_file = "./y.csv"

How to perform this step?

Annotate the parameters, input and outputs using CWL typing annotation.

a : 'CWLIntInput' = 5
b : 'CWLIntInput' = 4
c : 'CWLIntInput' = 6
input_file : 'CWLFilePathInput' = "./x.csv"
output_file : 'CWLFilePathOutput' = "./y.csv"

You can check the final notebook at

https://github.com/mosoriob/simpleModel-1/blob/master/simpleModelAnnotated.ipynb

Note

You will still be able to execute your notebook outside of MINT with the annotation.

Check your work

Run your notebook through https://mybinder.org and make sure it executes without error or human input at any step.

Next steps

In the next step, you will learn how to use MIC-web.