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.borroto@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.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_o... 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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On Wed, Oct 9, 2013 at 12:10 PM, UMD Bioinformatics <bioinformatics.umd@gmail.com> wrote:

Hi Carlos,

I've done some more tinkering and it seems that you are correct about passing the additional inputs. I can run the program with two inputs but if I use the repeat element $inputs on my command it fails. Where do I need to implement your suggestion? in the XML, or script, or both? Here is my updated XML file that works with just two inputs.

In your xml, this should work: <command interpreter ="python"> bkgd_sbtr_ian_properoutput.py $column $output1 $output1.id $input1 $input2 #for $i in $inputs ${i.input} #end for </command>