From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Thu, 5 Sep 2013 09:45:29 +0000 (+0100)
Subject: Improved help message
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=314fe48b43eae71cebe9eb76742ca586e2992837;p=jabaws.git

Improved help message
---

diff --git a/webservices/compbio/ws/client/Constraints.java b/webservices/compbio/ws/client/Constraints.java
index b9437f0..1c4283d 100644
--- a/webservices/compbio/ws/client/Constraints.java
+++ b/webservices/compbio/ws/client/Constraints.java
@@ -25,7 +25,7 @@ class Constraints {
 	final static String hostkey = "-h";
 	final static String servicekey = "-s";
 
-	final static String listServices = "-list_services";
+	final static String listServices = "-list";
 	final static String testKey = "-test";
 
 	// Actions
@@ -42,70 +42,51 @@ class Constraints {
 	final static String presetkey = "-r";
 
 	final static String help_text = "\r\n" + 
-			"JABAWS2 client August 2011 http://www.compbio.dundee.ac.uk/jabaws \r\n" + 
-			" \r\n" + 
-			"Usage: <Class or Jar file name> -h=host_and_context <-s=serviceName> ACTION [OPTIONS] \r\n" + 
-			"\r\n" + 
-			"-h=<host_context>  - a full URL to the JABAWS web server including context \r\n" + 
-			"                     path e.g. http://10.31.1.159:8080/ws\r\n" + 
-			"-s=<ServiceName>   - one of [MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, \r\n" + 
-			"					 ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS]\r\n" + 
-			"                     <serviceName> is required for all ACTIONS but -list_services\r\n" + 
+			"Usage: java -jar <JAR file name> -h=host_and_context <-s=serviceName> ACTION [OPTIONS] \r\n" + 
 			"\r\n" + 
+			"       -h=<host_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws\r\n" + 
+			"       -s=<ServiceName>  - a name of servise (the full list can be obtain with the option -list)\r\n" + 
+			"                           <serviceName> is required for all ACTIONS except -list\r\n\r\n" + 
 			"ACTIONS: \r\n" + 
-			"-list_services    - list available services\r\n" + 
-			"-test             - test service \r\n" + 
-			"-i=<inputFile>    - full path to fasta formatted sequence file, from which to align \r\n" + 
-			"                    sequences\r\n" + 
-			"-parameters       - lists parameters supported by web service\r\n" + 
-			"-presets          - lists presets supported by web service\r\n" + 
-			"-limits           - lists web services limits\r\n" + 
-			"\r\n" + 
-			"Please note that if input file is specified other actions are ignored\r\n" + 
-			"\r\n" + 
-			"OPTIONS (only for use with -i action):\r\n" + 
-			"-r=<presetName>   - name of the preset to use\r\n" + 
-			"-o=<outputFile>   - full path to the file where to write an alignment\r\n" + 
-			"-f=<PrmInputFile> - the name of the file with the list of parameters to use.\r\n" + 
-			"\r\n" + 
-			"Please note that -r and -f options cannot be used together. Alignment is done with \r\n" + 
-			"either preset or a parameters from the file, but not both!\r\n" + 
-			"\r\n" + 
-			"EXAMPLES: \r\n" + 
-			"\r\n" + 
-			"1) List all available services on the host \r\n" + 
-			"\r\n" + 
-			"Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -list_services\r\n" + 
-			"\r\n" + 
-			"2) Test Clustal web service \r\n" + 
-			"\r\n" + 
-			"Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=ClustalWS -test \r\n" + 
+			"        -i=<inputFile>  - defines an input file. For most services this is a FASTA file with initial sequences\r\n" + 
+			"        -list           - lists all available web services\r\n" + 
+			"        -test           - tests functioning of <ServiceName> \r\n" + 
+			"        -parameters     - lists parameters supported by <ServiceName>\r\n" + 
+			"        -presets        - lists presets supported by <ServiceName>\r\n" + 
+			"        -limits         - lists limits of <ServiceName>\r\n" + 
+			"\r\n" + 
+			"N.B. If an input file is specified with -i other actions are ignored!\r\n\r\n" + 
+			"OPTIONS (used with the -i action only):\r\n" + 
+			"        -r=<presetName>  - name of the preset to use\r\n" + 
+			"        -o=<outputFile>  - file with output results\r\n" + 
+			"        -f=<paramFile>   - file with the list of parameters to use.\r\n\r\n" + 
+			"Please note that -r and -f options cannot be used together. \r\n" + 
+			"Alignment/Prediction is done with either preset or a parameters from the file, but not both!\r\n\r\n" + 
+			"EXAMPLES: \r\n" +
+			"<THECLIENT> is java -jar <JAR file name>\r\n\r\n" +
+			"1) List all available services on the host:\r\n" + 
+			"   <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -list\r\n" + 
+			"\r\n" + 
+			"2) Test Clustal web service:\r\n" + 
+			"   <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=ClustalWS -test \r\n" + 
 			"\r\n" + 
 			"3) Align sequence from file input.txt with Probcons. Record resulting alignment \r\n" + 
-			"into the output.txt \r\n" + 
-			"\r\n" + 
-			"Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=ProbconsWS -i=input.txt -o=output.txt\r\n" + 
-			"\r\n" + 
-			"4) Calculate disorder with Disembl take input from input.txt, output results to \r\n" + 
-			"the console \r\n" + 
+			"   into the output.txt:\r\n" + 
+			"   <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=ProbconsWS -i=input.txt -o=output.txt\r\n" + 
 			"\r\n" + 
-			"Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=DisemblWS -i=input.txt \r\n" + 
+			"4) Calculate disorder with Disembl take input from input.txt with output results\r\n " +
+			"   to be printed out to the standard output:\r\n" + 
+			"    <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=DisemblWS -i=input.txt \r\n" + 
 			"\r\n" + 
-			"5) List all parameters available for AAconWS service \r\n" + 
-			"\r\n" + 
-			"Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -parameters\r\n" + 
+			"5) List all parameters available for AAconWS service:\r\n" + 
+			"   <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -parameters\r\n" + 
 			"\r\n" + 
 			"6) Calculate conservation with AAConWS using LANDGRAF method, for Clustal alignment \r\n" + 
-			"from input.txt and report  the scores to the console \r\n" + 
-			"\r\n" + 
-			"Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -i=input.txt -f=prm.txt \r\n" + 
-			"\r\n" + 
-			"Where the content of prm.txt file is -m=LANDGRAF\r\n" + 
-			"The list of the supported parameters can be obtained as shown in the example 5. \r\n" + 
+			"   from input.txt and report the scores to the standard output:\r\n" + 
+			"   <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -i=input.txt -f=prm.txt \r\n" + 
 			"\r\n" + 
-			"Citation: Peter V. Troshin, James B. Procter and Geoffrey J. Barton - \"Java \r\n" + 
-			"Bioinformatics Analysis Web Services for Multiple Sequence Alignment - \r\n" + 
-			"JABAWS:MSA\" Bioinformatics 2011; doi: 10.1093/bioinformatics/btr304.\r\n" + 
+			"   Where the content of prm.txt file is -m=LANDGRAF\r\n" + 
+			"N.B. The list of the supported parameters can be obtained as shown in the example 5.\r\n" + 
 			"";
 
 }