I am trying to implement workflow for the custom tool I developed inside galaxy . My tool has 2 input files one is treatment file and one is control. I am confused about how should I implement tht tool in galaxy
e.g i have 4 files input1,input2, chip1, chip2. 1. If I use input dataset option with chain like symbol it runs job with total 4 combinations (input1-chip1) (input1-chip2)(input2.chip1) (input-chip2) I only want (input1-chip1)(input-chip2)
I tried creating paired data but it gives me the error no bam paired data available .
How to run these 2 pairs in loops for workflow?