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