Hi Ian,

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
the form:"

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
this:
#for $i in $inputs
 ${i.input}
#end for

Hope it helps,
Carlos

On Wed, Oct 9, 2013 at 8:48 AM, UMD Bioinformatics
<bioinformatics.umd@gmail.com> wrote:

Hello,

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
http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
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.




Cheers
Ian

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