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acdvalid
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
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:6.6.0.0
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
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