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acdtable is used to create the table of parameters, allowed values and defaults, used in the application documentation and to provide user help.
% acdtable antigenic
Generate an HTML table of parameters from an application ACD file Version: EMBOSS:18.104.22.168 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
|Standard (Mandatory) qualifiers|
|Additional (Optional) qualifiers|
|Advanced (Unprompted) 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|
The output file is empty, but any format available to the specified program can be used.
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:
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:
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).
|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|
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.