I guess that is my point .. at a command prompt that can be achieved ( and gives the result they need ) but as far as I can see the same is not true via the Galaxy GUI ( unless there is a tool I am missing) They have 96 separate files to process hence the desire to use a workflow. Regards, Alistair -----Original Message----- From: Peter Cock [mailto:p.j.a.cock@googlemail.com] Sent: Thursday, 28 August 2014 2:27 PM To: Alistair Chilcott Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] BAM to SAM tool no way to get an unsorted SAM? Do you mean a SAM/BAM file sorted by read name? If so, try samtools sort -n ... instead. Peter On Thu, Aug 28, 2014 at 12:53 PM, Alistair Chilcott <Alistair.Chilcott@utas.edu.au> wrote:
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
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