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antigenic
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
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:6.6.0.0
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
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
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