Partitioning_environTreeFile00(((((sp1:1,sp2:1)L15:1,(sp3:1,sp4:1)L16:1)L7:1,((sp5:1,sp6:1)L17:1,(sp7:1,sp8:1)L18:1)L8:1)L3:1,(((sp9:1,sp10:1)L19:1,(sp11:1,sp12:1)L20:1)L9:1,((sp13:1,sp14:1)L21:1,(sp15:1,sp16:1)L22:1)L10:1)L4:1)L1:1,((((sp17:1,sp18:1)L23:1,(sp19:1,sp20:1)L24:1)L11:1,((sp21:1,sp22:1)L25:1,(sp23:1,sp24:1)L26:1)L12:1)L5:1,(((sp25:1,sp26:1)L27:1,(sp27:1,sp28:1)L28:1)L13:1,((sp29:1,sp30:1)L29:1,(sp31:1,sp32:1)L30:1)L14:1)L6:1)L2:1)L0:1;2013-05-07 08:22:39.918 UTCphylogenetic infernece in newick format of the sequences ( or clusters of sequences ) present in the different samples. Internal label are overwritten by the service. 2013-05-07 08:24:01.214 UTCSampleFile00clump1 1 sp1
clump1 1 sp2
clump1 1 sp3
clump1 1 sp4
clump1 1 sp5
clump1 1 sp6
clump1 1 sp7
clump1 1 sp8
clump2a 1 sp1
clump2a 1 sp2
clump2a 1 sp3
clump2a 1 sp4
clump2a 2 sp9
clump2a 2 sp10
clump2a 2 sp11
clump2a 2 sp12
clump2b 1 sp1
clump2b 1 sp2
clump2b 1 sp3
clump2b 1 sp4
clump2b 2 sp17
clump2b 2 sp18
clump2b 2 sp19
clump2b 2 sp20
clump4 1 sp1
clump4 1 sp2
clump4 1 sp9
clump4 1 sp10
clump4 2 sp17
clump4 2 sp18
clump4 2 sp25
clump4 2 sp26
even 1 sp1
even 1 sp5
even 1 sp9
even 1 sp13
even 1 sp17
even 1 sp21
even 1 sp25
even 1 sp29
random 1 sp2
random 2 sp5
random 1 sp12
random 4 sp14
random 2 sp15
random 3 sp17
random 1 sp22
random 2 sp24
2013-05-07 08:24:52.860 UTC a samplefile that show the where the leaf of the tree are found in the different sample and how many time.
It follows phylocom file input standard. text file with tree columns ( space or tab). First column sample name, second number of times the sequence found, the third the name of the sequence.2013-05-07 08:26:08.574 UTCSampleGroupingFile00The file define how sample should be grouped.
Text file in two columns ( space or tab). a line for each sample, first column the name of the sample, second the name of the group or state of the categorical variable.2013-05-07 08:27:58.246 UTCeven c
random q
clump2a a
clump2b a
clump4 a
clump1 a2013-05-07 08:26:44.514 UTCrandomization0010002013-04-11 11:01:10.921 UTCinsert an integer to define number of randomization to perform to estimate significance of the difference found across groups. Good rule of the thumb randomization = nlog(n) where n is the number of sequences.2013-05-07 08:29:40.598 UTCqparamHill00float larger than zero, define the diversity index to be used following Hill parametrization. 1 is shannon index2013-04-11 11:02:20.737 UTC12013-04-11 11:02:16.426 UTCoutputPrefix00Prefix for all outputfiles2013-04-11 11:03:23.959 UTCmyDiversity2013-04-11 11:03:07.610 UTCxmloutputType00Type of xml summary output type: two possible standard are used nexml and phyloxml. T
At the moment phyloxml is fully supported while nexml have some possible error2013-04-11 11:04:52.583 UTCphyloxml2013-04-11 11:05:01.158 UTCJobIDinteger that identify the job on the farm. Use it with the service centre to find out bug or crash of the job2013-05-07 09:02:18.812 UTCOutputPathLink to folder with all details of estimation2013-05-07 08:57:16.686 UTCURL2013-05-07 08:57:59.620 UTCStandardOuputURL of the HTML file of summary2013-05-07 08:57:48.151 UTCURL2013-05-07 08:57:54.927 UTCCall_Retrieve_PhyloHArgument0Name0JobID11Output_Path11Stadardouput22net.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.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.InvokeUpload_treeInputBody0File_name0REST_Service_redirection00net.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.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.InvokeUpload_sampleInputBody0File_name0REST_Service_redirection00net.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.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.InvokeUpload_sample_groupingInputBody0File_name0REST_Service_redirection00net.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.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.InvokeFormInput2PhyloHgroup0sample0tree0Nrandomization0qparamHill0XMLoutputType0output_prefix0output00net.sf.taverna.t2.activitieslocalworker-activity1.4net.sf.taverna.t2.activities.localworker.LocalworkerActivitytree0'text/plain'java.lang.Stringtruesample0'text/plain'java.lang.Stringtruegroup0text/plainjava.lang.StringtrueNrandomization0text/plainjava.lang.StringtrueqparamHill0text/plainjava.lang.Stringtrueoutput_prefix0text/plainjava.lang.StringtrueXMLoutputType0text/plainjava.lang.Stringtrueoutput00workfloworg.embl.ebi.escience.scuflworkers.java.StringConcatUserNameHere2013-04-11 11:34:07.948 UTCnet.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.InvokeServiceNamevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivityPhyloHnet.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.InvokeFile_name_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivitygroupnet.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.InvokeFile_name_value_1value00net.sf.taverna.t2.activitiesstringconstant-activity1.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivitysamplenet.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.InvokeFile_name_value_2value00net.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.InvokeInteractiondestination0net.sf.taverna.t2.activitiesinteraction-activity1.0.0net.sf.taverna.t2.activities.interaction.InteractionActivitydestination0text/plainjava.lang.Stringfalsehttp://www.mygrid.org.uk/taverna/internal/biovel/open_url.htmlLocallyPresentedHtmltruenet.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.InvokeCall_Retrieve_PhyloHArgumentCall_Retrieve_PhyloHNameUpload_treeInputBodyUpload_treeFile_nameUpload_sampleInputBodyUpload_sampleFile_nameUpload_sample_groupingInputBodyUpload_sample_groupingFile_nameFormInput2PhyloHgroupFormInput2PhyloHsampleFormInput2PhyloHtreeFormInput2PhyloHNrandomizationFormInput2PhyloHqparamHillFormInput2PhyloHXMLoutputTypeFormInput2PhyloHoutput_prefixInteractiondestinationJobIDOutputPathStandardOuputPartitioning environmental sequencing data using categorical and phylogenetic information using PhyloH .
The WF need a tree in newick format, a samplefile that show the where the leaf of the tree are found in the different sample and how many time, and a grouping file where the different sample are grouped using a categorical variable. The WF gives back a tabular and graphical representation of an entropy based partitioning of the information present in the sequence across the groupings, and a graphical and tabular representation of the contribution of each branch of the tree to the differentiation across groups of sample.
Further as side results the WF gives the tree annotated with the per branch contribution to the differentiation across groups of sample in nexml or phyloxml format and all files necessary to produce ex.novo the annotated tree on itol, giving the possibility to the user to add taxonomic information.
2013-05-07 08:19:04.918 UTCa17eb654-0171-4df2-ac36-4acc339384db2013-04-26 18:33:51.919 UTC7b6d374e-216b-4670-a68e-70afa004f63a2013-04-26 19:47:07.79 UTCb0dc1429-1970-4494-9f8c-f6d0be299c8a2013-04-11 11:34:13.925 UTCPartitioning environmental sequencing data using categorical and phylogenetic information using PhyloH 2013-05-07 08:12:14.626 UTC96567df7-67fb-41eb-86a5-eae0224dc36b2013-04-11 11:19:54.223 UTCsaverio vicario
giacinto Donvito
alfonso monaco
2013-05-07 08:11:03.170 UTC7fab7e35-85cf-4e21-bc13-995be24761e22013-05-07 08:30:14.602 UTC97fad68f-684e-43ba-b39c-8716ade2e1ad2013-05-07 08:19:06.317 UTCc41c6bc4-33ac-40f5-bd8b-93047b8dc1a92013-04-11 11:07:14.583 UTC09241519-d83d-4b4e-944c-e25e5b4bb3072013-05-07 09:02:29.484 UTCWorkflow1File_name00InputBody00REST_Service_responseBodyREST_Service_statusREST_Service_redirectionREST_Servicefile_name0inputBody0responseBody00status00redirection00net.sf.taverna.t2.activitiesrest-activity1.4net.sf.taverna.t2.activities.rest.RESTActivityPUThttp://testjst.ba.infn.it/openacces/{file_name}application/xmlapplication/xmlStringfalsetruefalsefalsetruefile_namejava.lang.Stringnet.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.InvokeREST_Servicefile_nameREST_ServiceinputBodyREST_Service_responseBodyREST_Service_statusREST_Service_redirection580e799c-bc6e-42d7-a347-e10430e1af0a2012-05-05 05:36:11.643 UTC517fa4a1-06ee-4bd7-980e-5f63e13c2fb22012-05-04 08:52:59.585 UTCacb3452e-6be0-4669-9e84-22808ff471cc2012-05-03 15:46:36.879 UTC99b23eb4-ca64-4f27-b08c-bdf3864724e52012-05-05 05:33:41.165 UTC24d62224-217d-46d0-a08a-06b0d60caec42012-05-02 07:59:24.107 UTCce6b1735-eb91-4d53-8e9b-ff43089857cd2012-05-02 12:54:46.975 UTC8513ae60-119a-414f-915e-bca0bb7a77342012-05-05 05:31:39.298 UTCd6bd51d4-54a3-4e41-ab79-ee29ecca40cf2012-05-03 15:34:45.183 UTC74b3d010-9e53-4df0-8513-43a9a1c30c862012-05-10 07:29:59.107 UTC8d4c37f0-a10b-465e-81aa-1c09938a34732012-05-01 08:37:47.922 UTCd56f22a8-96c1-4eb6-bf76-15cda0725ed82012-05-07 11:24:02.593 UTC2ee8114d-7999-4833-ba39-97ddb6ff067c2012-05-03 15:43:09.120 UTCb418f0df-28b8-497e-ac5d-a4b478911bd02012-05-01 08:36:38.8 UTCd1b49247-0c82-443c-acb1-bab1044296f42012-04-30 14:42:33.401 UTCd5aa2bb0-c984-456c-9ec2-df78463f19142012-05-01 08:39:00.787 UTCaff47fd7-0af5-47c0-afc2-a6f5ab27b5642012-04-30 14:16:40.142 UTC90744424-a1a0-4107-b358-5e931c677e4a2012-05-01 08:35:44.460 UTC49621bfe-01ef-4491-9a3e-d65911feb2a62012-05-24 16:26:53.940 UTC0ad720e2-8bbd-4aed-96f5-7563811739802012-04-24 12:19:06.97 UTC288673db-e11c-4f6a-be9c-57b0c212979d2012-04-30 14:48:27.139 UTC5d1ef777-4da0-4af7-abc1-938cbd13b6872012-05-05 05:39:03.774 UTCffce4883-3f94-487f-9c25-e2e7bcdeb2442012-05-06 19:42:14.223 UTCWorkflow14Name00Argument00StatusOutput_PathStadardouputJobIDREST_Servicename0arguments0responseBody00net.sf.taverna.t2.activitiesrest-activity1.4net.sf.taverna.t2.activities.rest.RESTActivityGEThttp://alicegrid17.ba.infn.it:8080/INFN.Grid.FrontEnd/services/QueryJob/InsertJobs?NAME={name}&arguments={arguments}application/xmlapplication/xmlStringfalsefalsefalsefalsetrueargumentsjava.lang.Stringnamejava.lang.Stringnet.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.InvokeXPath_Servicexml_text0nodelist11net.sf.taverna.t2.activitiesxpath-activity1.4net.sf.taverna.t2.activities.xpath.XPathActivity<?xml version="1.0" encoding="UTF-8"?>
<Job><Name>blast</Name><Flag>7772590c-d7ab-4b76-98b9-aa293c6c34fe</Flag><JobsID><JobId>454118</JobId></JobsID></Job>/Job/JobsID/JobIdnet.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.InvokeRetrivingJobJobID0Status00Output00StandardOutput11net.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>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
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