Example_for_external_tools_with_zip_and_unzipOriginal_File Parameter file for GROMACS downloaded directly from http://md.chem.rug.nl/~mdcourse/minim.mdp Any file would do for this example. 2011-05-18 09:07:51.93 BST Unzipped_File The compressed file is uncompressed again. 2011-05-18 09:01:18.7 BST unzip_STDERR Empty if executing normally. 2011-05-18 09:09:12.973 BST unzip_STDOUT Always empty. 2011-05-18 09:09:03.325 BST zip_STDERR Empty if executing normally. 2011-05-18 09:08:49.125 BST zip_STDOUT Always empty. 2011-05-18 09:08:55.373 BST diff_STDERRdiff_STDOUTZipped_filezipfile_to_zip0STDOUT00STDERR00zipped_file00net.sf.taverna.t2.activitiesexternal-tool-activity1.3net.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> http://taverna.nordugrid.org/sharedRepository/xml.php gzip zip unix:system Zipping single file zip archive.zip fred 1200 1800 file_to_zip fred true false true MacRoman false false false zipped_file archive.zip true false true true 0 true net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeunzipzipped_file0STDOUT00STDERR00unzipped_file00net.sf.taverna.t2.activitiesexternal-tool-activity1.3net.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> http://taverna.nordugrid.org/sharedRepository/xml.php gunzip unzip unix:system Unzipping single file unzip archive.zip 1200 1800 zipped_file archive.zip true false true MacRoman false false false unzipped_file fred true false true true 0 true net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_Web_Page_from_URLurl0contents00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivity url 0 'text/x-taverna-web-url' java.lang.String true base 0 'text/x-taverna-web-url' java.lang.String true contents 0 'text/plain,text/html' 0 workflow org.embl.ebi.escience.scuflworkers.java.WebPageFetcher net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeurl_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity http://www.myexperiment.org/files/135/download/franck.txt net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokedifffile10file20STDERR00STDOUT00net.sf.taverna.t2.activitiesexternal-tool-activity1.3net.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> ca6a7b10-3803-4586-9412-0892cffbcc7b diff file1 file2 1200 1800 file2 file2 true false false MacRoman false false false file1 file1 true false false MacRoman false false false false true true 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokezipfile_to_zipGet_Web_Page_from_URLcontentsunzipzipped_filezipzipped_fileGet_Web_Page_from_URLurlurl_valuevaluedifffile1Get_Web_Page_from_URLcontentsdifffile2unzipunzipped_fileOriginal_FileGet_Web_Page_from_URLcontentsUnzipped_Fileunzipunzipped_fileunzip_STDERRunzipSTDERRunzip_STDOUTunzipSTDOUTzip_STDERRzipSTDERRzip_STDOUTzipSTDOUTdiff_STDERRdiffSTDERRdiff_STDOUTdiffSTDOUTZipped_filezipzipped_file This workflow only works on a Unix machine. This workflow takes a fixed URL from which a text file is downloaded (output as Original_file). That file is zipped (output as Zipped_File) and then unzipped again (output as Unzipped_File). The orginal file and the unzipped version are then diff'd/ 2011-07-13 10:08:43.735 BST 5d81383a-33cb-42a3-a54a-0025c70e04d8 2011-05-18 08:59:20.533 BST 05976c99-c066-4b43-a8dc-a9d096460071 2011-05-10 17:32:49.50 BST ade60be2-6428-475c-9f67-f70563bc1859 2011-05-10 15:47:18.553 BST ab620d3b-2144-4b65-8b03-214f68413000 2011-07-13 10:06:07.77 BST 72fcee7c-a523-430e-84d6-545da6f20c10 2011-05-11 16:40:06.991 BST a48bb98d-73d6-4c42-b607-26f25fbf73b5 2011-07-13 10:09:25.490 BST 88042ede-d2fa-46bc-bb51-6f4365b377ea 2011-05-10 16:41:54.452 BST cb0a2a1a-8f24-4a5e-862a-c51044d59d83 2011-05-18 08:55:28.652 BST 2e3f8cd4-63db-4684-b10c-798aa671bbec 2011-05-18 09:09:16.597 BST 5a9d9e4d-b39d-4adc-ac18-105edfa55da5 2011-05-10 13:28:41.282 BST 204626f2-fa91-4efe-a12b-ceea66ebbe39 2011-05-10 15:27:04.848 BST f1f82722-871f-40b2-a143-9ec4b045e88d 2011-05-11 16:25:11.85 BST 9bd034c5-6356-4a02-8e46-339aaaba3900 2011-05-11 16:18:48.827 BST 26c1c5da-94bc-4945-a579-9af8d8b8a1ed 2011-05-18 09:08:00.646 BST ddf535eb-987c-441a-b807-42e48fd40c87 2011-05-13 16:57:36.108 BST 5def6db1-8ad5-4489-8fa7-13fb9d9b33d0 2011-05-11 16:17:16.379 BST 82bfd281-afe9-4136-b49b-90a9a0b3e9f1 2011-05-10 15:44:52.597 BST e01fa1b5-b659-4acc-8945-6bf40853d860 2011-07-13 10:01:28.45 BST 69681e3a-7113-492e-b6b2-0ed0a4aaab79 2011-05-10 17:31:13.719 BST 1ca4833e-fd69-4a11-9249-de0a0fc49508 2011-05-10 15:23:08.670 BST Example for external tools with zip and unzip 2011-07-13 10:06:44.403 BST 71961208-b9bc-4284-b163-b2c40eb4316b 2011-05-11 16:09:57.729 BST 96ac6bd6-084f-462b-8609-138c3fc02bef 2011-05-13 16:54:58.251 BST aafe4651-f880-431b-a11b-0791f3d53939 2011-05-11 16:39:39.7 BST Steffen Moeller Alan Williams 2011-05-18 08:56:32.351 BST 0bceac76-c220-4782-b776-4b270d31107a 2011-07-13 10:04:41.842 BST 5e75b9da-695e-4867-8aa8-4bf75c20e603 2011-05-10 17:09:18.46 BST