clustal_phylogenyalignment00accepts a clustalw protein sequence alignment2013-01-24 15:45:54.8 UTCCLUSTAL 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 UTCemail00Requires 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.
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If you use a fake email, the workflow may be cancelled before execution2013-01-24 15:32:05.472 UTCstatus_reportReports the status of the asynchronous service call2013-01-30 13:13:48.493 UTCFINISHED2013-01-30 13:13:55.153 UTCgetResult_treeProduces an phylogenetic tree in phylip format2013-01-30 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 UTCrunparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://www.ebi.ac.uk/Tools/services/soap/clustalw2_phylogeny?wsdlrunnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivityemail0'text/plain'falsetitle0'text/plain'falseparameters0'text/xml'falseoutput0'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=">run>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=">run>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=">run>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>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>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>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>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>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>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.Parallelize1net.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.Retry1.0100050000net.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.XMLOutputSplitterActivityinput0'text/xml'java.lang.StringfalsejobId0'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=">runResponse>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.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivitytree0'text/plain'falsekimura0'text/plain'falsetossgaps0'text/plain'falseclustering0'text/plain'falsepim0'text/plain'falsesequence0'text/plain'falseoutput0'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=">run>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>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>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>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>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>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>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.Parallelize1net.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.Retry1.0100050000net.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.Parallelize1net.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>truenet.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.Retry1.0100050000net.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.WSDLActivityhttp://www.ebi.ac.uk/Tools/services/soap/clustalw2_phylogeny?wsdlgetResultnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivityjobId0'text/plain'falsetype0'text/plain'falseparameters1'text/xml'falseoutput0'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=">getResult>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=">getResult>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=">getResult>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>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>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.Parallelize1net.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.Retry1.0100050000net.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.StringConstantActivitytreenet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLOutputSplitterActivityinput0'text/xml'java.lang.Stringfalseoutput0'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=">getResultResponse>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.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerunparametersrun_inputparametersrun_inputemailrun_outputinputrun_input_2sequencestatusJOB_IDgetResultparametersgetResult_inputtypegetResult_inputjobIdgetResult_outputinputstatus_reportgetResult_tree443dda04-ff00-466c-9e71-8b133d5cce8a2013-01-16 13:13:45.705 UTC918d4805-26ee-441e-bf28-a3a75f9f69f12013-01-30 13:13:59.303 UTC16fd2052-4591-4462-a5a9-5fbce75f4fad2013-01-24 15:46:57.896 UTC56c266b5-970f-4895-94a2-b969dff0917d2013-01-16 13:18:22.999 UTC8fc02eb6-3912-4487-87bc-ae31ee552bf12013-01-16 13:42:08.616 UTCc398cdfd-d999-4929-af67-b1d33974649f2013-01-16 13:42:46.931 UTCclustal_phylogeny2013-01-16 13:42:34.331 UTC5f98399f-4e3a-49c2-90ed-304d619f4b3a2013-01-24 15:32:07.122 UTCcfc27e98-1cf9-4d95-a4fe-aec9b5043b232013-01-25 09:44:53.162 UTC6eb99ce5-bc3d-486b-ad2a-d565becd2dbc2013-01-24 15:30:18.916 UTC632445e9-238d-4297-8565-b879c243e5642013-01-16 12:07:31.943 UTC651ce628-2792-4cb2-a278-8386d69851ba2013-01-16 13:16:11.852 UTCKaty Wolstencroft2013-01-16 13:42:46.176 UTC1670e09e-294a-4554-85d5-a0c16d5784712013-01-16 13:41:30.191 UTC0dd91d8e-414f-44e1-8840-fa42650c7ce52013-01-16 13:23:52.958 UTCab1cd5e1-fade-4329-be1f-0aa5f13080672013-01-30 13:11:10.742 UTCc647509f-a7fa-41ce-a44d-09e76af4056f2013-01-24 15:31:23.962 UTCThis 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 UTC7a509422-a069-41fc-ae01-34d90bd6af552013-01-16 13:11:09.281 UTCWorkflow18JOB_ID00statusgetStatusparameters0parameters00net.sf.taverna.t2.activitieswsdl-activity1.4net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://www.ebi.ac.uk/Tools/services/soap/clustalw2_phylogeny?wsdlgetStatusnet.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.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.Retry1.0100050000net.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.XMLInputSplitterActivityjobId0'text/plain'falseoutput0'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=">getStatus>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.Parallelize1net.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.Retry1.0100050000net.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.XMLOutputSplitterActivityinput0'text/xml'java.lang.Stringfalsestatus0'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=">getStatusResponse>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.Parallelize1net.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.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetStatusparametersgetStatus_inputjobIdgetStatus_outputinputstatus7dc29b15-f07e-4beb-9c34-2dc56e0355bb2013-01-16 11:53:30.48 UTC