Hello,

I've been working with a local installation of Galaxy and my question is
about how Galaxy chooses which file to use in the next step of the
workflow.

I have created a custom file type called "cub" which is required for my
custom tools and I have added this custom file type into the extension
list.  When I run the first step of my workflow, Galaxy will create an
intermediate cub file called dataset_51.dat.cub containing my processed
data, but also an empty intermediate dat file as well of the same name sans
cub extension (dataset_51.dat) .  The next tool in the workflow requires a
cub file type input, but instead of using the cub file, it chooses to
process the empty .dat file instead, causing the tool to process
incorrectly.

I've looked over some settings and double checked that my tool xml files
specify cub as the output file type and as the input file type for the next
tool, but now I am at a loss.  Is there anyway to specify to Galaxy that
the cub file should be used in the next step of the workflow instead of the
dat file?

Thank you very much for your help,

Kolby
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