I shall answer my own question. I found something remotely related when I googled the problem which put me on the right track.
As far as I'm concerned this is a somewhat ridiculous state of affairs, because I don't understand the need for this feature and I also don't understand why it is not documented in an obvious place.
When you upload a fasta file into a Galaxy history, you wil probably go to "Get Data" on the left hand menu and then "Upload File". When this file eventually appears in the history you can click on the little pencil icon to display its "attributes". In the "work area" of the Galaxy screen, that would be the middle section, the attributes of your files is displayed. However, "Attributes" is only one tab of the work area at this stage. There are also "Convert Format", "Datatype" and "Permissions". If one clicks on "Datatype", there is a heading, "New Type".
So since a fasta file was uploaded, the drop-down box displayes "fasta". Well, in my case it did. I won't be surprised if, for someone else, it displays something totally irrelivant. For bwa-mem this has to be changed to "fastqsanger". Why, I don't know? Until now I have never heard of a "fastqsanger" format file and having used bwa-mem regularly before on a cluster I have never come across this "type". But, since that is what Galaxy insists on, that is what you have to do. Something is then done to the file (what I don't know) because it does go off on a tangent for a while, the background of the file in the History becomes yellow, and then it is made available, when the background goes green again, and the file is available as an input in the dropbox to the bwa-mem tool.
I hope this helps someone else that is as stupid as me.
