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acdpretty will generate a correctly, fully formatted ACD file from one which is parsable but which is partly or incorrectly formatted.
acdpretty reads the ACD file and rewrites it with clean formatting to the file (ApplicationName).acdpretty which can be used to overwrite the original ACD file. The new file might contain many differences. For example, abbreviations will be expanded, all sections and attributes will be indented, all values will be quoted and lines will be wrapped at a reasonable width.
% acdpretty qatest Created qatest.acdpretty
Go to the output files for this example
All other command line parameters and qualifiers are essentially ignored as processing stops once the ACD file is printed. A few of the general qualifiers have the potential to conflict with the function of acdpretty.
Correctly reformat an application ACD file Version: EMBOSS:126.96.36.199 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 a pretty printed copy of the original ACD file.
All sections and attributed will be indented. All values will be quoted. Lines will be wrapped at a reasonable width.
The output file is intended as a standard format for parsers used by GUI and other interface wrappers, rather than using the original ACD file directly.
# Example ACD file for QA testing # application: qatest [ groups: "test" documentation: "ACD file for QA testing" ] sequence: asequence [ parameter: "Y" features: "Y" ] sequence: bsequence [ parameter: "Y" ] outfile: outfile [ parameter: "Y" ] integer: aint [ prompt: "first integer" ] integer: bint [ prompt: "second integer, first was $(aint)" default: "57" ] string: testalen [ standard: "Y" information: "asequence length $(asequence.length)" ] string: testblen [ standard: "Y" information: "bsequence length $(bsequence.length)" ] string: outdir [ information: "output directory" ] boolean: logic [ information: "boolean value" ] outfile: outtest [ parameter: "Y" odirectory: "$(outdir)" ] seqout: outseq [ parameter: "Y" features: "Y" osdirectory: "$(outdir)" ofdirectory: "$(outdir)" ]
acdpretty does not have its own options, but takes a single parameter which is the name of the ACD file that is being processed. It is invoked by specifying the name of the ACD file after the name of the utility application itself:
Any command line parameters that would normally be specified for the application are essentially ignored as processing stops once the reformatted ACD file is printed.
The format generated by acdpretty is intended as a standard for parsers used by GUI and other interface developers. It is far easier writing a parser to cope with acdpretty output than one which can cope with the ACD sytax in general.
A few of the global qualifiers have the potential to conflict with the function of acdpretty.
|acdc||Test 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)|
|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.