<?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>fconsense</serviceName>
		<organisation >
			<organisationName>European Bioinformatics Institute</organisationName>
		</organisation>

		<locationURL>http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_consensus.fconsense</locationURL>
		<interfaceWSDL>http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_consensus.fconsense?wsdl</interfaceWSDL>
		<serviceDescriptionText>Computes consensus trees by the majority-rule consensus tree method, which also allows one to easily find the strict consensus tree. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/embassy/phylipnew/fconsense.html</serviceDescriptionText>
		<operations >
			<serviceOperation >
				<operationName>fconsense</operationName>
				<operationDescriptionText>Computes consensus trees by the majority-rule consensus tree method, which also allows one to easily find the strict consensus tree. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/embassy/phylipnew/fconsense.html</operationDescriptionText>
				<operationInputs >
					<parameter >
						<parameterName>intreefile_direct_data</parameterName>
						<parameterDescription>Type: string. Phylip tree file. This is a mandatory parameter.&apos;intreefile_direct_data&apos;and&apos;intreefile_url&apos;are mutually exclusive.</parameterDescription>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>intreefile_url</parameterName>
						<parameterDescription>Type: string. Url of Phylip tree file. This is a mandatory parameter if&apos;intreefile_direct_data&apos;is not chosen.&apos;intreefile_direct_data&apos;and&apos;intreefile_url&apos;are mutually exclusive.</parameterDescription>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>method</parameterName>
						<parameterDescription>Type: string. Consensus method.This is an optional parameter. The allowed values for this parameter are: s(strict consensus tree)| mr(Majority Rule)| mre(Majority Rule (extended))| ml(Minimum fraction (0.5 to 1.0)). The default is&apos;mre&apos;</parameterDescription>
						<defaultValue>mre</defaultValue>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>mlfrac</parameterName>
						<parameterDescription>Type: float. Fraction (l) of times a branch must appear. The number is from 0.500 to 1.000. This is an optional parameter. The default is 0.5</parameterDescription>
						<defaultValue>0.5</defaultValue>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>root</parameterName>
						<parameterDescription>Type: boolean (Yes/No). Trees to be treated as Rooted. This is an optional parameter. The default is&apos;No&apos;.</parameterDescription>
						<defaultValue>N</defaultValue>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>outgrno</parameterName>
						<parameterDescription>Type: long. Species number to use as outgroup. This is an optional parameter. The default is 0</parameterDescription>
						<defaultValue>0</defaultValue>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>trout</parameterName>
						<parameterDescription>Type: boolean(Yes/No). Write out trees to tree file. This is an optional parameter. The default is&apos;Yes&apos;</parameterDescription>
						<defaultValue>Y</defaultValue>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>progress</parameterName>
						<parameterDescription>Type: boolean (true/false). Print indications of progress of run. This is an optional parameter. The default is&apos;true&apos;.</parameterDescription>
						<defaultValue>true</defaultValue>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>treeprint</parameterName>
						<parameterDescription>Type: boolean (true/false). Print out tree. This is an optional parameter. The default is&apos;true&apos;.</parameterDescription>
						<defaultValue>true</defaultValue>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>prntsets</parameterName>
						<parameterDescription>Type: boolean (true/false). Print out the sets of species. This is an optional parameter. The default is&apos;true&apos;</parameterDescription>
						<defaultValue>true</defaultValue>
						<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 a list of the species (in the order in which they appear in the first tree, which is the numerical order used in the program), a list of the subsets that appear in the consensus tree, a list of those that appeared in one or another of the individual trees but did not occur frequently enough to get into the consensus tree, followed by a diagram showing the consensus tree.</parameterDescription>
						<semanticType>http://www.mygrid.org.uk/ontology#phylogenetic_tree</semanticType>
						<transportDataType>String</transportDataType>
					</parameter>

					<parameter >
						<parameterName>outtreefile</parameterName>
						<parameterDescription>Returns consensus tree file.</parameterDescription>
						<transportDataType>String</transportDataType>
					</parameter>

				</operationOutputs>

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

		</operations>

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

</serviceDescriptions>
