JWS2 client

[jabaws.git] / webservices / compbio / ws / client / client_help.txt

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+\r
+JABAWS client v2.0 June 2011 http://www.compbio.dundee.ac.uk/jabaws \r
+ \r
+Usage: <Class or Jar file name> -h=host_and_context <-s=serviceName> ACTION [OPTIONS] \r
+\r
+-h=<host_context>  - a full URL to the JABAWS web server including context \r
+                     path e.g. http://10.31.1.159:8080/ws\r
+-s=<ServiceName>   - one of [MafftWS, MuscleWS, ClustalWS, TcoffeeWS, ProbconsWS, \r
+                     AAConWS, JronnWS, DisemblWS, GlobPlotWS]\r
+                     <serviceName> is required for all ACTIONS but -list_services\r
+\r
+ACTIONS: \r
+-list_services    - list available services\r
+-test             - test service \r
+-i=<inputFile>    - full path to fasta formatted sequence file, from which to align \r
+                    sequences\r
+-parameters       - lists parameters supported by web service\r
+-presets          - lists presets supported by web service\r
+-limits           - lists web services limits\r
+\r
+Please note that if input file is specified other actions are ignored\r
+\r
+OPTIONS (only for use with -i action):\r
+-r=<presetName>   - name of the preset to use\r
+-o=<outputFile>   - full path to the file where to write an alignment\r
+-f=<PrmInputFile> - the name of the file with the list of parameters to use.\r
+\r
+Please note that -r and -f options cannot be used together. Alignment is done with \r
+either preset or a parameters from the file, but not both!\r
+\r
+EXAMPLES: \r
+\r
+1) List all available services on the host \r
+\r
+Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -list_services\r
+\r
+2) Test Clustal web service \r
+\r
+Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=ClustalWS -test \r
+\r
+3) Align sequence from file input.txt with Probcons. Record resulting alignment \r
+into the output.txt \r
+\r
+Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=ProbconsWS -i=input.txt -o=output.txt\r
+\r
+4) Calculate disorder with Disembl take input from input.txt, output results to \r
+the console \r
+\r
+Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=DisemblWS -i=input.txt \r
+\r
+5) List all parameters available for AAconWS service \r
+\r
+Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -parameters\r
+\r
+6) Calculate conservation with AAConWS using LANDGRAF method, for Clustal alignment \r
+from input.txt and report  the scores to the console \r
+\r
+Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -i=input.txt -f=prm.txt \r
+\r
+Where the content of prm.txt file is -m=LANDGRAF\r
+The list of the supported parameters can be obtained as shown in the example 5. \r
+\r
+Citation: Peter V. Troshin, James B. Procter and Geoffrey J. Barton - "Java \r
+Bioinformatics Analysis Web Services for Multiple Sequence Alignment - \r
+JABAWS:MSA" Bioinformatics 2011; doi: 10.1093/bioinformatics/btr304.\r