- "-list_services - list available services\r\n" + \r
- "-test - test service \r\n" + \r
- "-i=<inputFile> - full path to fasta formatted sequence file, from which to align \r\n" + \r
- " sequences\r\n" + \r
- "-parameters - lists parameters supported by web service\r\n" + \r
- "-presets - lists presets supported by web service\r\n" + \r
- "-limits - lists web services limits\r\n" + \r
- "\r\n" + \r
- "Please note that if input file is specified other actions are ignored\r\n" + \r
- "\r\n" + \r
- "OPTIONS (only for use with -i action):\r\n" + \r
- "-r=<presetName> - name of the preset to use\r\n" + \r
- "-o=<outputFile> - full path to the file where to write an alignment\r\n" + \r
- "-f=<PrmInputFile> - the name of the file with the list of parameters to use.\r\n" + \r
- "\r\n" + \r
- "Please note that -r and -f options cannot be used together. Alignment is done with \r\n" + \r
- "either preset or a parameters from the file, but not both!\r\n" + \r
- "\r\n" + \r
- "EXAMPLES: \r\n" + \r
- "\r\n" + \r
- "1) List all available services on the host \r\n" + \r
- "\r\n" + \r
- "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -list_services\r\n" + \r
- "\r\n" + \r
- "2) Test Clustal web service \r\n" + \r
- "\r\n" + \r
- "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=ClustalWS -test \r\n" + \r
+ " -i=<inputFile> - defines an input file. For most services this is a FASTA file with initial sequences\r\n" + \r
+ " -list - lists all available web services\r\n" + \r
+ " -test - tests functioning of <ServiceName> \r\n" + \r
+ " -parameters - lists parameters supported by <ServiceName>\r\n" + \r
+ " -presets - lists presets supported by <ServiceName>\r\n" + \r
+ " -limits - lists limits of <ServiceName>\r\n" + \r
+ "\r\n" + \r
+ "N.B. If an input file is specified with -i other actions are ignored!\r\n\r\n" + \r
+ "OPTIONS (used with the -i action only):\r\n" + \r
+ " -r=<presetName> - name of the preset to use\r\n" + \r
+ " -o=<outputFile> - file with output results\r\n" + \r
+ " -f=<paramFile> - file with the list of parameters to use.\r\n\r\n" + \r
+ "Please note that -r and -f options cannot be used together. \r\n" + \r
+ "Alignment/Prediction is done with either preset or a parameters from the file, but not both!\r\n\r\n" + \r
+ "EXAMPLES: \r\n" +\r
+ "<THECLIENT> is java -jar <JAR file name>\r\n\r\n" +\r
+ "1) List all available services on the host:\r\n" + \r
+ " <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -list\r\n" + \r
+ "\r\n" + \r
+ "2) Test Clustal web service:\r\n" + \r
+ " <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=ClustalWS -test \r\n" + \r