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acdvalid |
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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.
% acdvalid antigenic |
Validate an application ACD file
Version: EMBOSS:6.5.0.0
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
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| 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 |
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:
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
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
| 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) |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.