Dear list,

I'm on galaxy-dist. I have a tool that outputs an unknown amount of files in a directory, all of which I need for input to the next tool. I used to tar them, but after a tip from John Chilton, I tried to fit this into Galaxy's composite datatypes. The tool now works, but I wonder if there is a better way to do it than how I have implemented it. I ran into some trouble when my new datatype's generate_primary_file was never called. (Is this only used after an upload?)


My tool now outputs to the output.extra_files_path given to it on the xml command line, and writes an HTML file to the output file it is given. The next tool reads input.extra_files_path, and uses the files there. In other words, no use has been made of add_composite_file, generate_primary_file, etc. I can even set composite_file=None in the datatype, and it will still work.

The whole thing feels a bit like a hack, so I wanted to ask if there is a way for tools to generate composite files the same way uploads can.

cheers,
jorrit boekel


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