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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

  • Outputs:

    • CWLFilePathOutput
    • CWLDumpableFile
    • CWLDumpableBinaryFile

Warning

the float datatype is currently not supported. Use a string input and coerce the string to float within the notebook.

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 mybinder.org and make sure it executes without error or human input at any step.