EMBOSS: acdtable manual

antigenic

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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

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
(none)
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
(none)
General qualifiers
-auto	boolean	Turn off prompts	Boolean value Yes/No	N
-stdout	boolean	Write first file to standard output	Boolean value Yes/No	N
-filter	boolean	Read first file from standard input, write first file to standard output	Boolean value Yes/No	N
-options	boolean	Prompt for standard and additional values	Boolean value Yes/No	N
-debug	boolean	Write debug output to program.dbg	Boolean value Yes/No	N
-verbose	boolean	Report some/full command line options	Boolean value Yes/No	Y
-help	boolean	Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose	Boolean value Yes/No	N
-warning	boolean	Report warnings	Boolean value Yes/No	Y
-error	boolean	Report errors	Boolean value Yes/No	Y
-fatal	boolean	Report fatal errors	Boolean value Yes/No	Y
-die	boolean	Report dying program messages	Boolean value Yes/No	Y
-version	boolean	Report version number and exit	Boolean value Yes/No	N

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