<?xml version = "1.0" encoding = "UTF-8"?>
<serviceDescriptions  xmlns="pd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="pd /C:/Documents and Settings/ytanoh/My Documents/TAVERNA/taverna-1.4-old/plugins/pedro/services/model/common.xsd">
	<serviceDescription >
		<serviceName>vrnadistance</serviceName>
		<organisation >
			<organisationName>European Bioinformatics Institute</organisationName>
		</organisation>

		<locationURL>http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_rna_folding.vrnadistance</locationURL>
		<interfaceWSDL>http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_rna_folding.vrnadistance?wsdl</interfaceWSDL>
		<serviceDescriptionText>RNA distances-calculates distances between RNA secondary structures. Detailed info about this operation can be found at the following link: http://lab.genomics.purdue.edu/cgi-bin/emboss/help/vrnadistance</serviceDescriptionText>
		<operations >
			<serviceOperation >
				<operationName>vrnadistance</operationName>
				<operationDescriptionText>RNA distances-calculates distances between RNA secondary structures. Detailed info about this operation can be found at the following link: http://lab.genomics.purdue.edu/cgi-bin/emboss/help/vrnadistance</operationDescriptionText>
				<operationInputs >
					<parameter >
						<parameterName>structure_direct_data</parameterName>
						<parameterDescription>Type: string. Vienna RNA structures file. This is a mandatory parameter if&apos;structure_url&apos;parameter is not chosen.</parameterDescription>
						<isConfigurationParameter>false</isConfigurationParameter>
						<semanticType>http://www.mygrid.org.uk/ontology#RNA_structure</semanticType>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>structure_url</parameterName>
						<parameterDescription>Type: string. Vienna RNA structures file. This is a mandatory parameter if&apos;structure_direct_data&apos;parameter is not chosen.</parameterDescription>
						<isConfigurationParameter>false</isConfigurationParameter>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>distance_f</parameterName>
						<parameterDescription>Type: boolean (true/false). Distance type: full (tree). This is an optional parameter. The default is&apos;true&apos;.</parameterDescription>
						<defaultValue>true</defaultValue>
						<isConfigurationParameter>false</isConfigurationParameter>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>distance_h</parameterName>
						<parameterDescription>Type: boolean (true/false). Distance type: hit (tree). This is an optional parameter. The default is&apos;false&apos;.</parameterDescription>
						<defaultValue>false</defaultValue>
						<isConfigurationParameter>false</isConfigurationParameter>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>distance_w</parameterName>
						<parameterDescription>Type: boolean (true/false). Distance type: Weighted coarse (tree). This is an optional parameter. The default is&apos;false&apos;.</parameterDescription>
						<defaultValue>false</defaultValue>
						<isConfigurationParameter>false</isConfigurationParameter>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>distance_c</parameterName>
						<parameterDescription>Type: boolean (true/false). Distance type: coarse (tree). This is an optional parameter. The default is&apos;false&apos;.</parameterDescription>
						<defaultValue>false</defaultValue>
						<isConfigurationParameter>false</isConfigurationParameter>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>distance_F</parameterName>
						<parameterDescription>Type: boolean (true/false). Distance type: full (string). This is an optional parameter. The default is&apos;false&apos;.</parameterDescription>
						<defaultValue>false</defaultValue>
						<isConfigurationParameter>false</isConfigurationParameter>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>distance_H</parameterName>
						<parameterDescription>Type: boolean (true/false). Distance type: hit (string). This is an optional parameter. The default is&apos;false&apos;.</parameterDescription>
						<defaultValue>false</defaultValue>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>distance_W</parameterName>
						<parameterDescription>Type: boolean (true/false). Distance type: Weighted coarse (string). This is an optional parameter. The default is&apos;false&apos;.</parameterDescription>
						<defaultValue>false</defaultValue>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>distance_C</parameterName>
						<parameterDescription>Type: boolean (true/false). Distance type: coarse (string). This is an optional parameter. The default is&apos;false&apos;.</parameterDescription>
						<defaultValue>false</defaultValue>
						<isConfigurationParameter>false</isConfigurationParameter>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>distance_P</parameterName>
						<parameterDescription>Type: boolean (true/false). Distance type: base pair distance. This is an optional parameter. The default is&apos;false&apos;.</parameterDescription>
						<defaultValue>false</defaultValue>
						<isConfigurationParameter>false</isConfigurationParameter>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>compare</parameterName>
						<parameterDescription>Type: string. Distance types to calculate. This is an optional parameter. The allowed values for this parameter are:p (Pairwise)|m (Distance matrix between all structures)|f (Compare all structures to the first one)|c (Compare continuously)|The default is&apos;p&apos;.</parameterDescription>
						<defaultValue>p</defaultValue>
						<isConfigurationParameter>false</isConfigurationParameter>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>schapiro</parameterName>
						<parameterDescription>Type: boolean (true/false). Use cost matrix for comparing coarse structures. This is an optional parameter. The default is&apos;false&apos;.</parameterDescription>
						<defaultValue>false</defaultValue>
						<isConfigurationParameter>false</isConfigurationParameter>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>doalignment</parameterName>
						<parameterDescription>Type: boolean (true/false). Alignment showing matching substructures. This is an optional parameter. The default is&apos;false&apos;.</parameterDescription>
						<defaultValue>false</defaultValue>
						<isConfigurationParameter>false</isConfigurationParameter>
						<transportDataType>String</transportDataType>
					</parameter>

				</operationInputs>

				<operationOutputs >
					<parameter >
						<parameterName>report</parameterName>
						<parameterDescription>Type: string. A general report for the underlying analysis job.</parameterDescription>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>detailed_status</parameterName>
						<parameterDescription>Type: long. The exit code of the underlying analysis job, 0 means the job returned normally.</parameterDescription>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>outfile</parameterName>
						<parameterDescription>Returns RNA secondary structure information</parameterDescription>
						<semanticType>http://www.mygrid.org.uk/ontology#RNA_structure</semanticType>
						<transportDataType>String</transportDataType>
					</parameter>

				</operationOutputs>

				<operationTask>http://www.mygrid.org.uk/ontology#calculating</operationTask>
			</serviceOperation>

		</operations>

		<serviceType>Soaplab service</serviceType>
	</serviceDescription>

</serviceDescriptions>
