I saw this page here:
Which describes how to load data from a file in order to output it ;
However, this is not what I want. In these examples, you would have to write out all your data into files and then load them back into output objects from files.
I want to be able to pass in any arbitrary input into a CommandLineTool, then pass that (or other) data back out, regardless of the involvement of any file. For example:
This is just a basic example with primitive data types, but ultimately what I would really like is the ability to pass in a
record type as an input, with one or more fields including
File objects, then inside my CommandLineTool do some processing to make a new file, and then output that same
record but with an updated
File in its fields.
I have tried writing this myself but I get syntax or “incorrect field” errors every time.
The CWL spec here describes several different
types's of CommandOutput and CommandOutputRecord object;
But I have not been able to find any real-world examples that show how to output anything from
CommandLineTool that is not from a file.