papplmaker.PLS(1) Analysis tools module generator


# get some help
papplmaker.PLS -h
# generate module for program 'seqret'
papplmaker.PLS -n edit.seqret
# ditto, but specify where to find 'seqret'
papplmaker.PLS -n edit::seqret
-l http://localhost:8080/axis/services
# ditto, but specify a non-default access method to 'seqret'
papplmaker.PLS -n edit::seqret
-a corba
# generate modules for all available analyses
# (using default location and default access method)
# do not generate but see what would be generated
papplmaker.PLS -s
papplmaker.PLS -S
# generate module for analysis 'edit::seqret'
# but name it 'MySeqret'
papplmaker.PLS -n edit::seqret -m MySeqret
# ...and use it
use MySeqret;
print new MySeqret->sequence_direct_data ('tatatacccgt')
->osformat ('embl')
# ditto but put the result into directory '/tmp/my'
# (directories do not need to exist)
papplmaker.PLS -n edit::seqret -m MySeqret -d /tmp/my/
# generate modules for all analysis whose names
# matches given regular expression (case insensitive)
papplmaker.PLS -r 'edit'
# ditto, but name generated module with your own names
# (letting papplmaker.PLS substitute parts of your names)
papplmaker.PLS -r 'edit' -m 'My_$ANALYSIS'


The module "Bio::Tools::Run::Analysis" provides access to the local and remote analysis tools in a unified way (defined in "Bio::AnalysisI"). The module uses general approach allowing to set arbitrary input data and to retrieve results by naming them. However, sometimes is more convenient to use a specific module, representing one analysis tool, that already knows about available input and result names.

The generator "papplmaker.PLS" creates such dedicated modules.

"papplmaker.PLS" uses the same access method as the general module - which means that depending on the parameter "access" it can use SOAP, CORBA or any other (supported) protocol, or it can access local analysis (available on the same machine where "papplmaker.PLS" is invoked).

"papplmaker.PLS" does its job either for one named analysis (specified by the "-n" option, or it uses "Bio::Tools::Run::AnalysisFactory" module in order to find what analyses are available, and can limit their number by matching against a regular expression given by the "-r" option.

The generated module or modules are named by default similarly to the names of the corresponding analyses, but this can be changed by the "-m" option which is actually a template where the following strings are recognised and replaced:

Will be replaced by the name of the analysis.
Will be replaced by the name of the category where the analysis belongs to.
Will be replaced by the entire name of the service (which is usually a concatenation of a category and a analysis name, and it is used also as a default module name, btw).

What is a difference between the "service" and "analysis", and what does "category" mean? Sometimes these terms may be confusing because they may mean slightly different things depending on the access method used to communicate with them. Generally, an "analysis" is a program (an application, a tool) running somewhere, but sometimes on a local machine. An example of an analysis is "seqret" (from the EMBOSS package). The analyses can be grouped into categories by their functions or by type of data they deal with (but sometimes there are no categories at all). Each analyses can be accessed using a higher level of abstraction, a "service". A service is usually a protocol-dependent wrapper, such as a Web Service, or a CORBA service. For example there is a "edit::seqret" service which represents analysis "seqret" in the category "edit".


Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  [email protected]                  - General discussion  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:


Martin Senger ([email protected])


Copyright (c) 2003, Martin Senger and EMBL-EBI. All Rights Reserved.

This script is free software; you can redistribute it and/or modify it under the same terms as Perl itself.


This software is provided ``as is'' without warranty of any kind.


None known at the time of writing this.