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JABAWS2 client August 2011 http://www.compbio.dundee.ac.uk/jabaws
Usage: <Class or Jar file name> -h=host_and_context <-s=serviceName> ACTION [OPTIONS]
-h=<host_context> - a full URL to the JABAWS web server including context
path e.g. http://10.31.1.159:8080/ws
-s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS,
ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS]
<serviceName> is required for all ACTIONS but -list_services
ACTIONS:
-list_services - list available services
-test - test service
-i=<inputFile> - full path to fasta formatted sequence file, from which to align
sequences
-parameters - lists parameters supported by web service
-presets - lists presets supported by web service
-limits - lists web services limits
Please note that if input file is specified other actions are ignored
OPTIONS (only for use with -i action):
-r=<presetName> - name of the preset to use
-o=<outputFile> - full path to the file where to write an alignment
-f=<PrmInputFile> - the name of the file with the list of parameters to use.
Please note that -r and -f options cannot be used together. Alignment is done with
either preset or a parameters from the file, but not both!
EXAMPLES:
1) List all available services on the host
Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -list_services
2) Test Clustal web service
Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=ClustalWS -test
3) Align sequence from file input.txt with Probcons. Record resulting alignment
into the output.txt
Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=ProbconsWS -i=input.txt -o=output.txt
4) Calculate disorder with Disembl take input from input.txt, output results to
the console
Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=DisemblWS -i=input.txt
5) List all parameters available for AAconWS service
Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -parameters
6) Calculate conservation with AAConWS using LANDGRAF method, for Clustal alignment
from input.txt and report the scores to the console
Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -i=input.txt -f=prm.txt
Where the content of prm.txt file is -m=LANDGRAF
The list of the supported parameters can be obtained as shown in the example 5.
Citation: Peter V. Troshin, James B. Procter and Geoffrey J. Barton - "Java
Bioinformatics Analysis Web Services for Multiple Sequence Alignment -
JABAWS:MSA" Bioinformatics 2011; doi: 10.1093/bioinformatics/btr304.
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