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>