                                  antigenic



Wiki

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   Please help by correcting and extending the Wiki pages.

Function

   Generate an HTML table of parameters from an application ACD file

Description

   acdtable is used to create the table of parameters, allowed values and
   defaults, used in the application documentation and to provide user
   help.

Usage

   Here is a sample session with acdtable


% acdtable antigenic


 Qualifier
 Type
 Description
 Allowed values
 Default



 Standard (Mandatory) qualifiers



 [-sequence]
(Parameter 1)
 seqall
 Protein sequence(s) filename and optional format, or reference (input USA)
 Readable sequence(s)
 Required



 -minlen
 integer
 Minimum length of antigenic region
 Integer from 1 to 50
 6



 [-outfile]
(Parameter 2)
 report
 Output report file name
 (default -rformat motif)
 <*>.antigenic



 Additional (Optional) qualifiers



 (none)



 Advanced (Unprompted) qualifiers



 (none)





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.

Generate an HTML table of parameters from 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

   Acdtable 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

   acdtable 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 after
   the name of the utility application itself:

   acdtable ApplicationName

   Acceptable expected and default values can be generated automatically
   for most ACD datatypes. In other cases, the allowed values is defined
   with the valid: global attribute, and the default value by the
   expected: global attribute (see EMBOSS Developers Manual).

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
                    acdtrace     Trace processing of an application ACD file (for testing)
                    acdvalid     Validate an application ACD file

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

Target users

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

Comments

                    None
