Pise/EMBOSS 2.3.1

[Catherine Letondal]

Hi,

I have more or less adapted new ACD types and attributes to Pise.
(ftp://ftp.pasteur.fr/pub/GenSoft/unix/misc/Pise/emboss_xml_files-2.3.1.tar.gz)

Main changes were for align types, where I could associate a "pipetype" to
chain to other programs taking alignment as input. BTW, I found "MSF" and "fasta" for the
-aformat parameter - are there others?

The main problem I had was with string parameters for specifying a path, with ./ default
value and having corresponding extn parameters.

On a Web interface you cannot really allow path and filename manipulation, and you 
must give a mean to the user to upload or input data (except if you have a login on user
home directory, which I'm aware is the choice for other Web interfaces for EMBOSS).
That's why I had to discard the following programs:
alignwrap, contacts, seqnr, seqsort, siggen, dichet and scopalign.

I have tried to "guess" that such parameter is a path, according to their name, 
with the next parameter being the extension, and, it's in the input or output section, 
so I can decide it's an InFile or Sequence, or Results Pise parameter. 
But some parameters are neither in input nor in output sections, and it's not secure 
to associate to parameters just because they follow each other.

A solution could be to have an explicit type and the extension as an attribute:

path: algpath  [
  parameter: "Y"
  prompt: "Location and extension of alignment files for input"
  default: "./"
  extn: ".align"
]

instead of (siggen.acd):

section: input [ info: "input Section" type: page ]
string: algpath  [
  parameter: "Y"
  prompt: "Location of alignment files for input"
  default: "./"
]

string: algextn  [
  parameter: "Y"
  prompt: "Extension of alignment files for input"
  default: ".align"
]

What do you think?

Thanks a lot in advance,

-- 
Catherine Letondal -- Pasteur Institute Computing Center