On Sun, Jan 27, 2013 at 10:26 PM, Kolby Chien <kc...@nau.edu> wrote:
> 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?

Galaxy wants all the files to use the names Galaxy tells the tool,
and those filenames all end with .dat - the problem is probably
Galaxy has told you (i.e. your tool) to use dataset_51.dat as the
output file, but your tool has instead used dataset_51.dat.cub
(which Galaxy will ignore).

Peter
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