Good afternoon, we are trying to create a reference from a WES dataset but the cnvkit analysis output file gives us 7 columns ( chromosome, start, end, Gene, log2, depth, spread). Although in the instruction it says that the input must be bam, in the platform there is only input for target and antitarget of the bed. It is necessary to transform all my BAM files using bedtools.
Welcome @valentina_ramirez
If I am understanding correctly, I think this is the first tool you will want to use instead (accepts the original BAM samples).
- CNVkit Autobin Estimates read counts or depths in a BAM file
From there, you can work with BED files, or you can run those BAM samples again with this tool.
- CNVkit Batch Run the CNVkit pipeline on one or more BAM files
Please give that a review and let us know if that is the right choice for what you want to do, and we can follow up more! 
These tools all work together and we can bring in more help for confirmation of the recommended path through the steps given how the tools were wrapped into Galaxy. All were recently created and a bit new without a lot of Galaxy-specific documentation yet. We can build that up here now as needed, and clarify if a tutorial (or workflow) is pending for later.