More than one output for EMBOSS apps

[Peter Rice]

James Bonfield wrote:
> This raises a related topic; how we determine what the output files are
> called?
> 
> For text outputs these are typically (always?) an option and can be set by the 
> user. For graphical outputs saved with -graph data the names are just
> generated. This has several problems:

I was planning to cover graph outputs in a later message.

You are right - any graph output with multiple files (*.png *.dat) will 
have this problem. -gdirectory helps, by letting you pecify where the 
files go, but you also need to know what files were written and have 
better control over the naming.

At present with graphs, -graph ps writes one files, but if you specify:

-graph data (or -graph png) -goutfile fred

You get fred1.dat (fred1.png) fred2.dat (fred2.png) and so on. 
Specifying -gdirectory jim (or EMBOSS_OUTDIRECTORY for all output files) 
will put those files in the jim/ directory.

It will also write a list of files to standard error, which you can trap 
and use to find the graphics output files.

Perhaps we can make this easier somehow?