[galaxy-dev] BAM to SAM tool no way to get an unsorted SAM?

Hello all,

My users are trying to use a tool called bismark and it requires an unsorted SAM file for one of its steps

Previous steps produce BAM files so we would like to include the tool BAM-to-SAM as a step in the workflow unfortunately it seems to be set to sort by default and there is no way to alter this behaviour.

Is there another tool that would convert a BAM to a SAM without sorting it or can the BAM-to-SAM tool be altered to include a checkbox for an unsorted result?

Regards,

Alistair