Change input binding to arguments in example files

[Fienne]

fixes #34

[swzCuroverse]

@Fienne -- so, this isn't how arguments work. You can't just unfortunately change input finding to arguments and how it work the same way. Unfortunately there isn't a really good section on arguments. Let me look and find some resources.-

[swzCuroverse]

You can see an explain here (some code that a co-worker wrote): https://github.com/arvados/l7g-ml/blob/main/PhasingImputation/Phasing/eagle.cwl

[swzCuroverse]

@tetron thoughts on this ticket do you have information about when to up inputBinding vs arguments and some resources? I will admit I always use inputBinding.

[Fienne]

You can see an explain here (some code that a co-worker wrote): https://github.com/arvados/l7g-ml/blob/main/PhasingImputation/Phasing/eagle.cwl

Thank you @swzCuroverse . I'll need to take sometime on this one 😅

[tetron]

The interaction between inputBinding and arguments is described here:

https://www.commonwl.org/v1.2/CommandLineTool.html#Input_binding

The arguments field is separate from inputs, but has the same inputBinding type.

arguments is usually simpler, it is a plain list of command line arguments and values more like you would write in other programming languages. However it separates the definition of the input parameter from the definition of command line parameter it corresponds to, so if you have a large number of possible options (some bioinformatics tools have dozens of flags) can be more maintainable to define them together.