Create_nanopublicatiruby_script_path00 path to the ruby script (the ruby script canbe downloaded from : 2015-04-03 21:00:03.936 UTC input_file_path00 path to the input file 2015-04-03 20:57:30.607 UTC output_file_path00 path where the nanopubs should be stored 2015-04-03 20:57:22.543 UTC data_row_start_position00 the number of the row where the data starts 2015-04-03 20:57:10.98 UTC entrezId_column_number00 the column number of the table where the gene ids are stored 2015-04-03 20:56:57.605 UTC outputerrorrun_nanopub_ruby_scriptrubyScript0outputPath0inputPath0dataRowStartPosition0entrezIdColumnNumber0STDOUT00STDERR00net.sf.taverna.t2.activitiesexternal-tool-activity1.4net.sf.taverna.t2.activities.externaltool.ExternalToolActivity 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local <?xml version="1.0" encoding="UTF-8"?> <localInvocation><shellPrefix>/bin/sh -c</shellPrefix><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand></localInvocation> 1996397d-d1aa-46de-8635-3ccffd8b9d78 # variables inputFileName=%%inputPath%% outputFilePath=%%outputPath%% dataRowStartPosition=%%dataRowStartPosition%% entrezIdColumnNumber=%%entrezIdColumnNumber%% echo $(ruby %%rubyScript%% --input ${inputFileName} --output ${outputFilePath} --data_row_start_position ${dataRowStartPosition} --entrez_id_column_number ${entrezIdColumnNumber}) 1200 1800 dataRowStartPosition entrezIdColumnNumber inputPath outputPath rubyScript entrezIdColumnNumber entrezIdColumnNumber false false false UTF-8 false false false rubyScript rubyScript false false false UTF-8 false false false outputPath outputPath false false false UTF-8 false false false inputPath inputPath false false false UTF-8 false false false dataRowStartPosition dataRowStartPosition false false false UTF-8 false false false false true true 0 false 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_nanopub_ruby_scriptrubyScriptruby_script_pathrun_nanopub_ruby_scriptoutputPathoutput_file_pathrun_nanopub_ruby_scriptinputPathinput_file_pathrun_nanopub_ruby_scriptdataRowStartPositiondata_row_start_positionrun_nanopub_ruby_scriptentrezIdColumnNumberentrezId_column_numberoutputrun_nanopub_ruby_scriptSTDOUTerrorrun_nanopub_ruby_scriptSTDERR 5baf84fc-e479-4cd2-830e-b64da5c8999f 2015-04-03 21:10:48.318 UTC 75a49a60-ab8b-4519-9234-132924564933 2015-03-30 09:09:28.670 UTC fe601804-d7ae-4a62-96f5-74ed18a4d01a 2015-03-30 09:37:08.99 UTC b8d0aae6-5ff6-4e51-95a3-77313e7f0ca3 2015-03-30 09:02:56.980 UTC This workflow creates nanopublications for a gene list that is associated to Huntington's Disease 2015-04-03 21:11:49.507 UTC 11d0763c-cf94-4531-b33d-e7fa30d82f1c 2015-03-30 09:26:01.986 UTC 556e33f2-dde2-45ff-b57c-f9618e0c7e28 2015-03-30 09:36:20.652 UTC 3b79bfd2-2daa-4354-bbf3-cdea82afb312 2015-03-30 08:56:57.147 UTC 8b9f39e3-2f7a-41f5-9cb4-8f98bb12c21d 2015-03-30 09:44:27.171 UTC eddd3ff8-3190-47c9-99e3-9789d5d47ee6 2015-03-30 09:13:46.981 UTC 55300c1c-c88a-4191-92a1-d455131b34c5 2015-03-30 08:58:37.699 UTC 6f872052-1708-48dd-8ae0-f33dbadc4036 2015-03-30 09:31:03.899 UTC 49cdfeee-e24c-4ffb-b954-ef8d14176b55 2015-03-30 09:32:45.95 UTC e0846b61-1d95-41ca-b136-e56bccc276fe 2015-04-03 20:57:08.796 UTC feebecc8-66fa-4764-99a3-e5981a1463f5 2015-04-03 21:10:44.911 UTC Rajaram Kaliyaperumal 2015-04-03 21:10:06.134 UTC 2f3dc96e-df91-4551-a992-2632ed2a3ff2 2015-03-30 09:40:02.410 UTC 5f89ff9f-cea6-43d1-9c06-f49eb553d67f 2015-03-30 08:55:10.180 UTC 0a9883b3-8faa-4ec1-86ab-71c4e3549fd6 2015-04-03 21:14:06.383 UTC Create nanopublications 2015-04-03 21:11:57.371 UTC 15251c74-f655-4775-bb79-b20d18721f10 2015-03-30 09:29:08.677 UTC 066a8117-904b-4125-a965-6d922ca66189 2015-03-30 09:16:12.923 UTC 3a4350fe-83da-464c-a05c-44782edf1405 2015-04-03 21:11:56.20 UTC 6de4f3d4-2d75-4104-9edd-b7cfd1aba94c 2015-04-03 21:02:59.741 UTC 38748080-3419-4d69-a5b7-6815bd35b7ec 2015-03-30 09:19:23.460 UTC 1c7b6092-398d-4909-9881-a630ba393733 2015-03-30 09:06:17.148 UTC e948b657-a8a5-414b-81d6-d926d136a33e 2015-03-30 09:26:35.717 UTC