On Wed, Oct 9, 2013 at 12:10 PM, UMD Bioinformatics
<bioinformatics....@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
    #end for

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