
                                 acdvalid 



Function

   Validate an application ACD file

Description

   acdvalid processes an ACD file and reports any errors or warnings
   caused by incorrect, deprecated or obsolete syntax. The tests go above
   and beyond those of acdc and acdtrace. It highlights ACD syntax that
   might cause problems to third-party parsing software which wrap the
   EMBOSS applications.

   acdvalid validates the ACD file, testing many features which will not
   prevent an application from running, but will create problems for the
   interfaces, whether on the command-line or some other type.

Usage

   Here is a sample session with acdvalid


% acdvalid antigenic 

Command line arguments

   The first parameter is the name of the program to compile. All other
   command line parameters and qualifiers are defined for that program -
   see the documentation for the program of choice.

Output file format

   The output file is empty, but any format available to the specified
   program can be used.

Data files

   Acdvalid will use any data files specified in the ACD file of the
   specified program, but will ignore any data files that are only used
   directly by the program's code.

   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by the EMBOSS
   environment variable EMBOSS_DATA.

   To see the available EMBOSS data files, run:

% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata".
   Files for all EMBOSS runs can be put in the user's home directory, or
   again in a subdirectory called ".embossdata".

   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

Notes

   acdvalid does not have its own options, but takes a single parameter
   which is the name of the EMBOSS application that is being testsed. It
   is invoked by specifying the name of the application to be tested
   along with any command-line options after the name of the utility
   application itself:

   acdvalid ApplicationName Options

   acdvalid will run the command line interface of any EMBOSS program by
   reading its ACD file and processing the command line and user
   responses in exactly the same way as if the true program itself were
   running. The application proper is not run; it is only the ACD file
   that is read.Any command-line options for the application being called
   can be specified. The user is prompted for any required values for
   application parameters and any input files are read. Output files can
   be specified in any available format however they will be empty (the
   application code is not called so there will be no output).

   acdvalid will use any data files specified in the ACD file of the
   specified program, but will ignore any data files that are only used
   directly by the program's code. EMBOSS data files are distributed with
   the application and stored in the standard EMBOSS data directory (see
   EMBOSS Users Manual for further information).

   acdvalid generates both error and warning messages. If the message is
   an "Error" then the ACD file will not work and requires fixing. Most
   of the messages from acdvalid are "Warnings" and do not prevent a
   program from running, however it is still worth trying to fix the
   problem.

   Although the warning messages are only advisory, as many warnings as
   possible are fixed for any application in the main release. Further
   validation tests will be added in future releases so it is worth
   running acdvalid on all local ACD files with each new version of
   EMBOSS

References

Warnings

   None.

Diagnostic Error Messages

Exit status

   It exits with status 0.

Known bugs

   None.

See also

   Program name Description
   acdc Test an application ACD file
   acdpretty Correctly reformat an application ACD file
   acdtable Generate an HTML table of parameters from an application ACD
   file
   acdtrace Trace processing of an application ACD file (for testing)

Author(s)

   Peter Rice (pmr © ebi.ac.uk)
   Informatics Division, European Bioinformatics Institute, Wellcome
   Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

History

   Written 2004

Target users

   This program is intended to be used by developers of applications and
   interfaces.

Comments

   None
