Hi Carlos,

Well first I fixed my typo but it still doesn't work. I do have my 
universe_wsgi.ini set to use the job_working_directory and I've test this with 
a functional script to make sure that was not the issue. I found the $inputs 
XML setup in another Galaxy script. It takes the additional files but maybe 
it's not passing them properly? 

This is the error I'm getting
/bin/sh: galaxy.tools.DatasetFilenameWrapper: No such file or directory

Ian
On Oct 9, 2013, at 10:11 AM, Carlos Borroto <carlos.borr...@gmail.com>
 wrote:

> 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....@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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