                                  acdvalid



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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.

Validate an application ACD file
Version: EMBOSS:6.5.6.0

   Standard (Mandatory) qualifiers: (none)
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers: (none)
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit


Input file format

   The input is whatever the chosen application reads.

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
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

   Written 2004

Target users

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

Comments

   None
