bionic (1) bp_papplmaker.pl.1p.gz

NAME

       papplmaker.PLS -  Analysis tools module generator

SYNOPSIS

         # 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
                    -l http://corba.ebi.ac.uk/IOR/Analyses.ref
                    -a corba

         # generate modules for all available analyses
         # (using default location and default access method)
         papplmaker.PLS

         # 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')
                               ->wait_for
                               ->outseq;

         # 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'

DESCRIPTION

       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:

       $ANALYSIS or ${ANALYSIS}
           Will be replaced by the name of the analysis.

       $CATEGORY or ${CATEGORY}
           Will be replaced by the name of the category where the analysis belongs to.

       $SERVICE or ${SERVICE}
           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".

FEEDBACK

   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.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - 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:

         http://redmine.open-bio.org/projects/bioperl/

AUTHOR

       Martin Senger (senger@ebi.ac.uk)

COPYRIGHT

       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.

DISCLAIMER

       This software is provided "as is" without warranty of any kind.

BUGS AND LIMITATIONS

       None known at the time of writing this.