You can work around this using the from_work_dir attribute when specifying the 
output file in your tool config.

-- jt 

(composed on my phone)

On Jan 27, 2013, at 6:13 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:

> 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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