I'm new to Galaxy. I have Chip-seq data for two cell types. Each cell type has two replicates. I already ran an alignment workflow in galaxy with bwa for each of the replicates. Now, I want to make a peak calling workflow. When editing my workflow, I put two input data boxes to represent each replicate for a cell type. I then put a merge BAM files, connecting the outputs of the input files to the inputs of the Merge BAM files box. I then connected Merge BAM files to Call Peaks Using Macs.

My questions:

When I went to run my workflow, I was unable to select from the drop down menu under "input data" the two different replicates of a single cell type. The drop down menu was actually empty.

I then went to my work history that contained my aligned data, and the drop down menu only gave me the option of selecting the "aligned with bwa" and the converted SAM to BAM output of the ONE replicate. So, I couldn't put the aligned BAM file of one replicate in one input box and the aligned BAM file of another replicate in the other input box, so I could merge the BAM files to run through MACS.

How can I merge the aligned BAM files of two different replicates for a cell type to call peaks using Macs in Galaxy?

Is there a different way you suggest I approach this workflow for chip-seq peak calling using Macs.