If you want to have a way to specify rules that use the same command, but still specify the rules manually, look up "!macros" in `man tup`. If the issue is that the commands need to write and read some temp files, then note that you can write temp files in a tup command (they need to be placed in $TMPDIR iirc). Note that the tup command can be calling a script that you place alongside, in case this makes specifying your sequences of commands easier. You can define the macro in top-level Tuprules.tup and use include_rules in all the Tupfiles to get it included.
Does this fail to address your problem?