clustal_phylogenyalignment00 accepts a clustalw protein sequence alignment 2013-01-24 15:45:54.8 UTC CLUSTAL 2.1 multiple sequence alignment sp|P00560|PGK_YEAST MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|G2WA29|G2WA29_YEASK MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|E7QC39|E7QC39_YEASZ MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|E7KA32|E7KA32_YEASA MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|C8Z499|C8Z499_YEAS8 MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|C7GQM4|C7GQM4_YEAS2 MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|B3LU83|B3LU83_YEAS1 MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|A6ZTJ3|A6ZTJ3_YEAS7 MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|E7LRY4|E7LRY4_YEASV MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV tr|H0GD00|H0GD00_9SACH MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYV ************************************************** sp|P00560|PGK_YEAST LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|G2WA29|G2WA29_YEASK LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|E7QC39|E7QC39_YEASZ LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|E7KA32|E7KA32_YEASA LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|C8Z499|C8Z499_YEAS8 LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|C7GQM4|C7GQM4_YEAS2 LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|B3LU83|B3LU83_YEAS1 LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|A6ZTJ3|A6ZTJ3_YEAS7 LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|E7LRY4|E7LRY4_YEASV LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG tr|H0GD00|H0GD00_9SACH LEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVG ************************************************** sp|P00560|PGK_YEAST PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|G2WA29|G2WA29_YEASK PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|E7QC39|E7QC39_YEASZ PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|E7KA32|E7KA32_YEASA PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|C8Z499|C8Z499_YEAS8 PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|C7GQM4|C7GQM4_YEAS2 PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|B3LU83|B3LU83_YEAS1 PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|A6ZTJ3|A6ZTJ3_YEAS7 PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|E7LRY4|E7LRY4_YEASV PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH tr|H0GD00|H0GD00_9SACH PEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRH ************************************************** sp|P00560|PGK_YEAST ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|G2WA29|G2WA29_YEASK ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|E7QC39|E7QC39_YEASZ ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|E7KA32|E7KA32_YEASA ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|C8Z499|C8Z499_YEAS8 ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|C7GQM4|C7GQM4_YEAS2 ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|B3LU83|B3LU83_YEAS1 ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|A6ZTJ3|A6ZTJ3_YEAS7 ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|E7LRY4|E7LRY4_YEASV ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE tr|H0GD00|H0GD00_9SACH ELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALE ************************************************** sp|P00560|PGK_YEAST NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|G2WA29|G2WA29_YEASK NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|E7QC39|E7QC39_YEASZ NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|E7KA32|E7KA32_YEASA NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|C8Z499|C8Z499_YEAS8 NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|C7GQM4|C7GQM4_YEAS2 NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|B3LU83|B3LU83_YEAS1 NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|A6ZTJ3|A6ZTJ3_YEAS7 NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|E7LRY4|E7LRY4_YEASV NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE tr|H0GD00|H0GD00_9SACH NPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTE ************************************************** sp|P00560|PGK_YEAST IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|G2WA29|G2WA29_YEASK IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|E7QC39|E7QC39_YEASZ IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|E7KA32|E7KA32_YEASA IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|C8Z499|C8Z499_YEAS8 IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|C7GQM4|C7GQM4_YEAS2 IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|B3LU83|B3LU83_YEAS1 IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|A6ZTJ3|A6ZTJ3_YEAS7 IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|E7LRY4|E7LRY4_YEASV IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT tr|H0GD00|H0GD00_9SACH IGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVT ************************************************** sp|P00560|PGK_YEAST DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|G2WA29|G2WA29_YEASK DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|E7QC39|E7QC39_YEASZ DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|E7KA32|E7KA32_YEASA DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|C8Z499|C8Z499_YEAS8 DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|C7GQM4|C7GQM4_YEAS2 DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|B3LU83|B3LU83_YEAS1 DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|A6ZTJ3|A6ZTJ3_YEAS7 DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|E7LRY4|E7LRY4_YEASV DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT tr|H0GD00|H0GD00_9SACH DKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGT ************************************************** sp|P00560|PGK_YEAST KALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|G2WA29|G2WA29_YEASK KALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|E7QC39|E7QC39_YEASZ KALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|E7KA32|E7KA32_YEASA KALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|C8Z499|C8Z499_YEAS8 KALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|C7GQM4|C7GQM4_YEAS2 KALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|B3LU83|B3LU83_YEAS1 KALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|A6ZTJ3|A6ZTJ3_YEAS7 KALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|E7LRY4|E7LRY4_YEASV KALLXEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL tr|H0GD00|H0GD00_9SACH KALLEEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLEL **** ********************************************* sp|P00560|PGK_YEAST LEGKELPGVAFLSEKK tr|G2WA29|G2WA29_YEASK LEGKELPGVAFLSEKK tr|E7QC39|E7QC39_YEASZ LEGKELPGVAFLSEKK tr|E7KA32|E7KA32_YEASA LEGKELPGVAFLSEKK tr|C8Z499|C8Z499_YEAS8 LEGKELPGVAFLSEKK tr|C7GQM4|C7GQM4_YEAS2 LEGKELPGVAFLSEKK tr|B3LU83|B3LU83_YEAS1 LEGKELPGVAFLSEKK tr|A6ZTJ3|A6ZTJ3_YEAS7 LEGKELPGVAFLSEKK tr|E7LRY4|E7LRY4_YEASV LEGKELPGVAFLSEKK tr|H0GD00|H0GD00_9SACH LEGKELPGVAFLSEKK **************** 2013-01-25 09:44:50.267 UTC email00 Requires a valid email address in order to execute services hosted at the EBI. The EBI asks for an email address so that they can contact you about: Problems with the service which affect your jobs. Scheduled maintenance which affects services you are using. Deprecation and retirement of a service you are using. If you use a fake email, the workflow may be cancelled before execution 2013-01-24 15:32:05.472 UTC status_report Reports the status of the asynchronous service call 2013-01-30 13:13:48.493 UTC FINISHED 2013-01-30 13:13:55.153 UTC getResult_tree Produces an phylogenetic tree in phylip format 2013-01-30 13:12:54.98 UTC ( ( ( ( ( ( sp|P00560|PGK_YEAST:0.00000, tr|G2WA29|G2WA29_YEASK:0.00000) :0.00000, tr|E7QC39|E7QC39_YEASZ:0.00000) :0.00000, ( tr|E7LRY4|E7LRY4_YEASV:0.00120, tr|H0GD00|H0GD00_9SACH:0.00120) :0.00120) :0.00000, ( tr|E7KA32|E7KA32_YEASA:0.00000, tr|C8Z499|C8Z499_YEAS8:0.00000) :0.00000) :0.00000, tr|C7GQM4|C7GQM4_YEAS2:0.00000) :0.00000, tr|B3LU83|B3LU83_YEAS1:0.00000, tr|A6ZTJ3|A6ZTJ3_YEAS7:0.00000); 2013-01-30 13:12:32.778 UTC runparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.ebi.ac.uk/Tools/services/soap/clustalw2_phylogeny?wsdl run net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_inputparameters0email0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity email 0 'text/plain' false title 0 'text/plain' false parameters 0 'text/xml' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="run" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}run"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="email" qname="&gt;run&gt;email"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>User email address</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="string" name="title" qname="&gt;run&gt;title"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>A title to identify the analysis job</xsd:documentation></xsd:annotation></s:basetype><s:complextype optional="false" unbounded="false" typename="InputParameters" name="parameters" qname="&gt;run&gt;parameters"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>The list of parameters to be used for launching the analysis</xsd:documentation></xsd:annotation><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="tree" qname="InputParameters&gt;tree"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Tree Format [Determines the outputs that ClustalW produces.]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="boolean" name="kimura" qname="InputParameters&gt;kimura"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Distance correction [Controls whether ClustalW attempts to correct for multiple substitutions at the same site. This is recommended to be set 'on' for more divergent sequences and has the effect of stretching branch lengths. For very divergent sequences the distances cannot be reliably corrected.]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="boolean" name="tossgaps" qname="InputParameters&gt;tossgaps"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Excludes Gaps [With this option enabled columns where any of the sequences in the input have a gap will be excluded, forcing the alignment to use only positions where information can be included from all sequences.]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="string" name="clustering" qname="InputParameters&gt;clustering"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Clustering Methods [Clustering Methods]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="boolean" name="pim" qname="InputParameters&gt;pim"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Percent Identity Matrix [Output the percentage identity matrix]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters&gt;sequence"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Sequence [Phylogeny using an alignment directly entered into the input box in a supported format. Alignment formats supported include Clustal, FASTA and MSF. Partially formatted or unaligned sequences are not accepted. Adding a return to the end of the sequence may help ClustalW understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present. There is currently a limit of 500 sequences and 1MB of data.]</xsd:documentation></xsd:annotation></s:basetype></s:elements></s:complextype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_outputinput0jobId00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false jobId 0 'text/plain' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="runResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}runResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname="&gt;runResponse&gt;jobId"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>A unique identifier for the analysis job</xsd:documentation></xsd:annotation></s:basetype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerun_input_2sequence0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity tree 0 'text/plain' false kimura 0 'text/plain' false tossgaps 0 'text/plain' false clustering 0 'text/plain' false pim 0 'text/plain' false sequence 0 'text/plain' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="InputParameters" name="parameters" qname="&gt;run&gt;parameters"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>The list of parameters to be used for launching the analysis</xsd:documentation></xsd:annotation><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="tree" qname="InputParameters&gt;tree"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Tree Format [Determines the outputs that ClustalW produces.]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="boolean" name="kimura" qname="InputParameters&gt;kimura"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Distance correction [Controls whether ClustalW attempts to correct for multiple substitutions at the same site. This is recommended to be set 'on' for more divergent sequences and has the effect of stretching branch lengths. For very divergent sequences the distances cannot be reliably corrected.]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="boolean" name="tossgaps" qname="InputParameters&gt;tossgaps"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Excludes Gaps [With this option enabled columns where any of the sequences in the input have a gap will be excluded, forcing the alignment to use only positions where information can be included from all sequences.]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="string" name="clustering" qname="InputParameters&gt;clustering"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Clustering Methods [Clustering Methods]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="boolean" name="pim" qname="InputParameters&gt;pim"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Percent Identity Matrix [Output the percentage identity matrix]</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="true" unbounded="false" typename="string" name="sequence" qname="InputParameters&gt;sequence"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Sequence [Phylogeny using an alignment directly entered into the input box in a supported format. Alignment formats supported include Clustal, FASTA and MSF. Partially formatted or unaligned sequences are not accepted. Adding a return to the end of the sequence may help ClustalW understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present. There is currently a limit of 500 sequences and 1MB of data.]</xsd:documentation></xsd:annotation></s:basetype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokestatusJOB_ID0status00net.sf.taverna.t2.activitiesdataflow-activity1.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Loop <activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns=""> <inputs> <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> <name>status</name> <depth>0</depth> <translatedElementType>java.lang.String</translatedElementType> <allowsLiteralValues>true</allowsLiteralValues> </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean> </inputs> <outputs> <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean> <name>loop</name> <depth>0</depth> <granularDepth>0</granularDepth> </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean> </outputs> <classLoaderSharing>workflow</classLoaderSharing> <localDependencies /> <artifactDependencies /> <script>loop = "" + status.equals("RUNNING"); if ("true".matches(loop)) { Thread.sleep(500); }</script> <dependencies /> </net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity> true net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetResultparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.ebi.ac.uk/Tools/services/soap/clustalw2_phylogeny?wsdl getResult net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetResult_inputtype0jobId0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity jobId 0 'text/plain' false type 0 'text/plain' false parameters 1 'text/xml' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResult" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResult"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname="&gt;getResult&gt;jobId"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>An identifier for the job to check</xsd:documentation></xsd:annotation></s:basetype><s:basetype optional="false" unbounded="false" typename="string" name="type" qname="&gt;getResult&gt;type"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>The renderer to be used to format the output</xsd:documentation></xsd:annotation></s:basetype><s:arraytype optional="true" unbounded="false" wrapped="false" typename="wsRawOutputParameters" name="parameters" qname="&gt;getResult&gt;parameters"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>A list of parameters to be passed on to the renderer</xsd:documentation></xsd:annotation><s:elementtype><s:complextype optional="false" unbounded="false" typename="wsRawOutputParameter" name="" qname="{http://soap.jdispatcher.ebi.ac.uk}wsRawOutputParameter"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="name" qname="wsRawOutputParameter&gt;name"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>The name of the parameter</xsd:documentation></xsd:annotation></s:basetype><s:arraytype optional="false" unbounded="false" wrapped="true" typename="ArrayOfString" name="value" qname="wsRawOutputParameter&gt;value"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>The parameter value as an array of String</xsd:documentation></xsd:annotation><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoketype_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity tree net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetResult_outputinput0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false output 0 'application/octet-stream' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getResultResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getResultResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="base64Binary" name="output" qname="&gt;getResultResponse&gt;output"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>Base64 encoded data corresponding to the output of the job formatted by the renderer</xsd:documentation></xsd:annotation></s:basetype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerunparametersrun_inputoutputrun_inputparametersrun_input_2outputrun_inputemailemailrun_outputinputrunparametersrun_input_2sequencealignmentstatusJOB_IDrun_outputjobIdgetResultparametersgetResult_inputoutputgetResult_inputtypetype_valuevaluegetResult_inputjobIdrun_outputjobIdgetResult_outputinputgetResultparametersstatus_reportstatusstatusgetResult_treegetResult_outputoutput 443dda04-ff00-466c-9e71-8b133d5cce8a 2013-01-16 13:13:45.705 UTC 918d4805-26ee-441e-bf28-a3a75f9f69f1 2013-01-30 13:13:59.303 UTC 16fd2052-4591-4462-a5a9-5fbce75f4fad 2013-01-24 15:46:57.896 UTC 56c266b5-970f-4895-94a2-b969dff0917d 2013-01-16 13:18:22.999 UTC 8fc02eb6-3912-4487-87bc-ae31ee552bf1 2013-01-16 13:42:08.616 UTC c398cdfd-d999-4929-af67-b1d33974649f 2013-01-16 13:42:46.931 UTC clustal_phylogeny 2013-01-16 13:42:34.331 UTC 5f98399f-4e3a-49c2-90ed-304d619f4b3a 2013-01-24 15:32:07.122 UTC cfc27e98-1cf9-4d95-a4fe-aec9b5043b23 2013-01-25 09:44:53.162 UTC 6eb99ce5-bc3d-486b-ad2a-d565becd2dbc 2013-01-24 15:30:18.916 UTC 632445e9-238d-4297-8565-b879c243e564 2013-01-16 12:07:31.943 UTC 651ce628-2792-4cb2-a278-8386d69851ba 2013-01-16 13:16:11.852 UTC Katy Wolstencroft 2013-01-16 13:42:46.176 UTC 1670e09e-294a-4554-85d5-a0c16d578471 2013-01-16 13:41:30.191 UTC 0dd91d8e-414f-44e1-8840-fa42650c7ce5 2013-01-16 13:23:52.958 UTC ab1cd5e1-fade-4329-be1f-0aa5f1308067 2013-01-30 13:11:10.742 UTC c647509f-a7fa-41ce-a44d-09e76af4056f 2013-01-24 15:31:23.962 UTC This workflow accepts a ClustalW protein sequence alignment and produces a phylogenetic tree, using the EBI clustalw_phylogeny web service, which implements phylip. 2013-01-24 15:44:27.698 UTC 7a509422-a069-41fc-ae01-34d90bd6af55 2013-01-16 13:11:09.281 UTC Workflow18JOB_ID00statusgetStatusparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.ebi.ac.uk/Tools/services/soap/clustalw2_phylogeny?wsdl getStatus net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetStatus_inputjobId0output00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity jobId 0 'text/plain' false output 0 'text/xml' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getStatus" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getStatus"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="jobId" qname="&gt;getStatus&gt;jobId"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>An identifier for the job to check</xsd:documentation></xsd:annotation></s:basetype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetStatus_outputinput0status00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity input 0 'text/xml' java.lang.String false status 0 'text/plain' 0 <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getStatusResponse" name="parameters" qname="{http://soap.jdispatcher.ebi.ac.uk}getStatusResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="status" qname="&gt;getStatusResponse&gt;status"><xsd:annotation xmlns:xsd="http://www.w3.org/2001/XMLSchema"><xsd:documentation>The status of the job (FINISHED, ERROR, RUNNING, NOT_FOUND or FAILURE)</xsd:documentation></xsd:annotation></s:basetype></s:elements></s:complextype></s:extensions> net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetStatusparametersgetStatus_inputoutputgetStatus_inputjobIdJOB_IDgetStatus_outputinputgetStatusparametersstatusgetStatus_outputstatus 7dc29b15-f07e-4beb-9c34-2dc56e0355bb 2013-01-16 11:53:30.48 UTC