[Bioperl-l] biopipe/Pipeline Manager

[matthieu CONTE]

Hello,
I  working on Biopipe by using Pipeline Manager. I work with modified 
version of "phylip_tree_pipeline.xml"
http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-pipeline/xml/examples/xml/phylip_tree_pipeline.xml?cvsroot=bioperl

My problem is that I do not have only one input file but 1128  differents 
files in input !

My input files are multifasta with a set of protein from Arabidopsis 
thaliana and Oryza sativa
containing a specific PFAM motif.
The path for example for the motif PF00012 is:  
/PF00012/fasta_PF00012/PF00012.fa and so on for the 1128 motifs.

What I want to do is to loop on the 1128 PFAM files.

Enter the PFAM number in a let's say $pf

Start the job with the Path /$pf/fasta_$pf/$pf.fa file

But I don't find any way to work with a non global variable
Does somebody have an idea?
Is it possible to modify Pipeline Manager so that it can hang argument an 
input file?

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