As far as I can tell you problem could be the files not being written
to the right place. From the link you posted:
"To use this method at least one output dataset (output1 in our
example) must be specified - this dataset will act as the reference
for our additional datasets. The new additional datasets must be
placed in the directory provided by $__new_file_path__ and named in
Although there is also this possibility:
"Alternately, if your universe_wsgi.ini has collect_outputs_from =
job_working_directory, moving the files into $__new_file_path__ is not
needed and only the naming form above is required."
Please confirm you have the proper setting in universe_wsgi.ini or try
telling your tool to write all outputs files to $__new_file_path__.
Also, I didn't know you could use $inputs(a repeat element definition
in your xml) in that way. I thought you needed to do something like
#for $i in $inputs
Hope it helps,
On Wed, Oct 9, 2013 at 8:48 AM, UMD Bioinformatics
> I'm trying to incorporate a python tool that can accommodate multiple input
> files and the number of output files cannot be determined prior to running
> the tool. I've been though the help section at
> but I'm not getting any results. The tool isn't even running and creating
> the proper output in the tool directory. I've felt with the naming
> convention requited by Galaxy and the tool works from the command line. I
> know that the issue isn't with my local Galaxy install because a generic
> tool I've installed that produces multiple outputs works fine. I've attached
> my code and the XML file. Any help would be appreciated.
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