[Bioperl-pipeline] xml dir housekeeping -- No hardcoding

[Juguang Xiao]

> On writing pipeline tests, pipeline tests should  be file based, meaning
> it doesn't assume the availability of biosql or ensembl or other schema. Also
> no hardcoding.  Within the xml, one can add the various adaptors and stuff but commented out
> for testing purposes. Users who want to use the templates, should make a copy
> and uncomment or modify accordingly.

Hi Shawn,

It is hard to define the standard of whether it is hardcoding or not. :) One idea is that you are non hardcoding if you refer to the files that reside only in t/data/. Or you have a bette definition.

In XML, we can use DTD entity to make such template, say.

<!-- change to your own path -->
<!ENTITY file_path "/usr/juguang/backyard/dna_piece.fa">

And in the xml file, we write like this.

<file>&file_path;</file>

When you use this pipeline, you just need to modify the entity like.

<!ENTITY file_path "/usr/shawn/data/another_dna_piece.fa">

That is what entity is supposed to do. Cool, right? ;) However, this feature needs to be supported by the parser, while I did not test it on XML::Parser yet. Let me make it test later.

Juguang.