EMBL-EBI Web Services

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====== Kalign (SOAP) ======

===== Description =====

Kalign ((Lassmann T., Frings O. and Sonnhammer E.L. (2009)\\
**Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features.**\\
Nucleic Acids Research 37(3):858-65\\ 
PubMed: [[http://europepmc.org/abstract/MED/19103665|19103665]]\\ 
DOI [[http://dx.doi.org/10.1093/nar/gkn1006|10.1093/nar/gkn1006]]\\ 
)) is a fast and accurate multiple sequence alignment algorithm for DNA and protein sequences.

For more information see:
  * Web form: [[http://www.ebi.ac.uk/Tools/msa/kalign/]]
  * [[.:Kalign (REST)|REST service]]
  * [[http://msa.sbc.su.se/|Kalign homepage]]

Web service registry entries:
  * [[http://www.biocatalogue.org/services/2183|BioCatalogue]]
  * [[http://www.programmableweb.com/api/ebi-kalign|ProgrammableWeb.com]]

===== Important ====

We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of up to 25 at a time and to not submit more until the results and processing has completed for these. This enables users as well as the service maintainers to deal more easily with local and remote network outages as well as scheduled or unscheduled downtime.

Service provision happens on a fair-share basis. Overzealous usage of a particular resource will be dealt with in accordance to the [[http://www.ebi.ac.uk/about/terms-of-use|EMBL-EBI's Terms of Use]].

===== Clients =====

Sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.

^ Language ^ Download ^ Requirements ^
^ C# | .NET Executable: ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/bin/KalignCliClient.exe|KalignCliClient.exe]]''; Source: ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/EBIWS2_CSharp/EbiWS/AbstractWsClient.cs|AbstractWsClient.cs]]'', ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/EBIWS2_CSharp/EbiWS/KalignClient.cs|KalignClient.cs]]'', ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/csharp/EBIWS2_CSharp/KalignCliClient/KalignCliClient.cs|KalignCliClient.cs]]'' | A .NET runtime environment. If building from source development tools are also required. See the [[tutorials:06_Programming:dot_net|.NET tutorial]] for details. |
^ Java | Executable jar: ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/java/jar/Kalign_Axis1.jar|Kalign_Axis1.jar]]''; Source: ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/java/src/uk/ac/ebi/webservices/AbstractWsToolClient.java|AbstractWsToolClient.java]]'', ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/java/src/uk/ac/ebi/webservices/axis1/KalignClient.java|KalignClient.java]]'' | [[http://ws.apache.org/axis/|Axis 1.4]]; All dependencies, including [[http://ws.apache.org/axis/|Axis 1.4]] and [[http://commons.apache.org/cli/|Commons-CLI]], are available in ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/java/lib-1.4.zip|lib-1.4.zip]]''. |
^ Perl | ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/perl/soaplite/kalign_soaplite.pl|kalign_soaplite.pl]]'' | [[http://search.cpan.org/perldoc?SOAP::Lite|SOAP::Lite]] |

For further details of these tool-kits and workflow platforms see our [[:tutorials:00_Contents|Guide to Web Services]].

===== WSDL =====

The [[http://www.w3.org/TR/wsdl|WSDL]] for the Kalign SOAP service: http://www.ebi.ac.uk/Tools/services/soap/kalign?wsdl

===== Operations =====

==== getParameters() ====

Get a list of the parameter names.

Arguments: //none//

Returns: a list of strings giving the names of the parameters.

==== getParameterDetails(parameterId) ====

Get details of a specific parameter.

Arguments:
  * ''parameterId'': identifier/name of the parameter to fetch details of.

Returns: a [[#wsParameterDetails]] describing the parameter and its values.

==== run(email, title, params) ====

Submit a job to the service.

Arguments:
  * ''email'': (**required**) user e-mail address. See [[help:faq#why_do_you_need_my_e-mail_address|Why do you need my e-mail address?]]
  * ''title'': job title. Default: "".
  * ''params'': (**required**) parameters for the tool. These are described by the [[#InputParameters]] data structure.

Returns: a string containing the job identifier (''jobId'').

==== getStatus(jobId) ====

Get the status of a submitted job.

Arguments:
  * ''jobId'': (**required**) job identifier.

Returns: a string containing the status.

The values for the status are:
  * ''RUNNING'': the job is currently being processed.
  * ''FINISHED'': job has finished, and the results can then be retrieved.
  * ''ERROR'': an error occurred attempting to get the job status.
  * ''FAILURE'': the job failed.
  * ''NOT_FOUND'': the job cannot be found.
Further details can be found in [[:tutorials:01_intro#jdispatcher|Synchronous and Asynchronous Access: JDispatcher]].

==== getResultTypes(jobId) ====

Get the available result types for a finished job.

Arguments:
  * ''jobId'': (**required**) job identifier.

Returns: a list of [[#wsResultType]] data structures describing the available result types.

==== getResult(jobId, type, parameters) ====

Get the result of a job of the specified type.

Arguments:
  * ''jobId'': (**required**) job identifier.
  * ''type'': (**required**) string specifying the result type to fetch. See [[#getResultTypes(jobId)]] for details of the available types.
  * ''parameters'': optional list of [[#wsRawOutputParameter]] used to provide additional parameters for derived result types.

Returns: the result data for the specified type, base64 encoded. Depending on the SOAP library and programming language used the result may be returned in decoded form. For some result types (e.g. images) this will be binary data rather than a text string.

===== Data Types =====

==== InputParameters ====

The input parameters for the job:

^ Attribute        ^ Type    ^ Description ^
| ''stype''        | string  | input sequence type. |
| ''sequence''     | string  | sequences to align. |
| ''format''       | string  | output alignment format. |
| ''gapopen''      | real    | gap creation penalty. |
| ''gapext''       | real    | gap extension penalty. |
| ''termgap''      | real    | terminal gap penalty. |
| ''bonus''        | real    | bonus score. |

More detailed information about each parameter, including valid values  can be obtained using the [[#getParameterDetails(parameterId)]] operation.

==== wsParameterDetails ====

Descriptive information about a tool parameter. Returned by [[#getParameterDetails(parameterId)]].

^ Attribute       ^ Type   ^ Description ^
| ''name''        | string | Name of the parameter. |
| ''description'' | string | Description of the parameter, suitable for use in option help interfaces. |
| ''type''        | string | Data type of the parameter. |
| ''values''      | list of [[#wsParameterValue]] | List of valid values for the option. |

==== wsParameterValue ====

Description of a tool parameter value. Used in [[#wsParameterDetails]].

^ Attribute       ^ Type     ^ Description ^
| ''label''        | string  | Display name of the value, for use in interfaces. |
| ''value''        | string  | String representation of the value to be passed to the tool parameter. |
| ''defaultValue'' | boolean | Flag indicating if this value is the default. |
| ''properties''   | list of [[#wsProperty]] | List of key/value pairs providing further information. |

==== wsProperty ====

Properties of a tool parameter value. Used in [[#wsParameterValue]].

^ Attribute ^ Type   ^ Description ^
| ''key''   | string | |
| ''value'' | string | |

==== wsRawOutputParameter ====

Additional parameters passed when requesting a result. See [[#getResult(jobId, type, parameters)]].

^ Attribute ^ Type           ^ Description ^
| ''name''  | string         | |
| ''value'' | list of string | |

==== wsResultType ====

Description of a result type. Returned by [[#getResultTypes(jobId)]].

^ Attribute       ^ Type   ^ Description ^
| ''identifier''  | string | Identifier for the result type. Passed as ''type'' to [[#getResult(jobId, type, parameters)]]. |
| ''label''       | string | Display name for use in user interfaces. |
| ''description'' | string | Description of the result type, for use in help interfaces. |
| ''mediaType''   | string | MIME type of the returned data. |
| ''fileSuffix''  | string | Suggested suffix for file name, if writing data to disk. |
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