Workflow1dir_of_mzML_files00pepproph_out0comet_out0protproph_out0excel_out0html_out0mzid_out0csv_out0comet_peptide_searchdir_of_mzML_files0STDOUT00net.sf.taverna.t2.activitiesexternal-tool-activity1.5net.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> f6865e2a-435a-4b80-8491-7b8b5f6de5e5 cd %%dir_of_mzML_files%% comet *.mzML 1200 1800 dir_of_mzML_files dir_of_mzML_files dir_of_mzML_files false false false UTF-8 false false false false true false 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePeptideProphetdir_of_mzML_files0STDOUT00net.sf.taverna.t2.activitiesexternal-tool-activity1.5net.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> ebd1c0c5-822e-4a49-9fdf-619b76e06103 cd %%dir_of_mzML_files%% for i in *.pep.xml; do PeptideProphetParser $i; done 1200 1800 dir_of_mzML_files dir_of_mzML_files dir_of_mzML_files false false false UTF-8 false false false false true false 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeProteinProphetdir_of_mzML_files0STDOUT00net.sf.taverna.t2.activitiesexternal-tool-activity1.5net.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> d681fd06-31e1-4749-9e48-43ec56a4cec4 cd %%dir_of_mzML_files%% for i in *.pep.xml; do ProteinProphet $i $i.prot.xml NOGROUPS; done 1200 1800 dir_of_mzML_files dir_of_mzML_files dir_of_mzML_files false false false UTF-8 false false false false true false 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecreate_excel_filedir_of_mzML_files0STDOUT00net.sf.taverna.t2.activitiesexternal-tool-activity1.5net.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> b1e3b4c3-7785-4acf-b7f5-b048ffdaf2cf cd /usr/local/tpp/bin for i in %%dir_of_mzML_files%%/*.prot.xml; do protxml2html -file $i EXCEL; done 1200 1800 dir_of_mzML_files dir_of_mzML_files dir_of_mzML_files false false false UTF-8 false false false false true false 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecreate_html_filedir_of_mzML_files0STDOUT00net.sf.taverna.t2.activitiesexternal-tool-activity1.5net.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> b1e3b4c3-7785-4acf-b7f5-b048ffdaf2cf cd /usr/local/tpp/bin for i in %%dir_of_mzML_files%%/*.prot.xml; do protxml2html -file $i HTML; done 1200 1800 dir_of_mzML_files dir_of_mzML_files dir_of_mzML_files false false false UTF-8 false false false false true false 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecreate_mzIdentML_filedir_of_mzML_files0STDOUT00net.sf.taverna.t2.activitiesexternal-tool-activity1.5net.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> b1e3b4c3-7785-4acf-b7f5-b048ffdaf2cf cd %%dir_of_mzML_files%% for i in *.prot.xml; do IDFileConverter -in $i -out $i.mzid; done 1200 1800 dir_of_mzML_files dir_of_mzML_files dir_of_mzML_files false false false UTF-8 false false false false true false 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecreate_csv_filesdir_of_mzML_files0STDOUT00net.sf.taverna.t2.activitiesexternal-tool-activity1.5net.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> b1e3b4c3-7785-4acf-b7f5-b048ffdaf2cf cd %%dir_of_mzML_files%% for i in *.xls; do ssconvert $i $i.csv; done 1200 1800 dir_of_mzML_files dir_of_mzML_files dir_of_mzML_files false false false UTF-8 false false false false true false 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecomet_peptide_searchdir_of_mzML_filesdir_of_mzML_filesPeptideProphetdir_of_mzML_filesdir_of_mzML_filesProteinProphetdir_of_mzML_filesdir_of_mzML_filescreate_excel_filedir_of_mzML_filesdir_of_mzML_filescreate_html_filedir_of_mzML_filesdir_of_mzML_filescreate_mzIdentML_filedir_of_mzML_filesdir_of_mzML_filescreate_csv_filesdir_of_mzML_filesdir_of_mzML_filespepproph_outPeptideProphetSTDOUTcomet_outcomet_peptide_searchSTDOUTprotproph_outProteinProphetSTDOUTexcel_outcreate_excel_fileSTDOUThtml_outcreate_html_fileSTDOUTmzid_outcreate_mzIdentML_fileSTDOUTcsv_outcreate_csv_filesSTDOUT 2d52b1a0-cc46-41fe-be86-5a8be60f909b 2015-08-13 05:23:07.666 UTC 39980618-9c84-4796-a5d5-e09dbd4cac91 2015-08-15 00:25:24.123 UTC bef29dcc-8d0d-4684-9b3f-45fb88ece6f0 2015-08-13 02:52:41.609 UTC 2a4f59d4-e75e-4b5c-ae45-72aac6d140b5 2015-08-13 03:13:43.793 UTC 6a2f30c1-9b57-4060-a294-2dcda4dfd86c 2015-08-15 00:56:22.945 UTC b06c2f45-217a-43b9-83d2-15045f2e6d0b 2015-08-13 04:18:37.655 UTC c1911763-f94e-4748-824a-33f5c1c372cb 2015-08-13 04:46:22.14 UTC af1666fc-5d6d-4c83-bb7c-4455f1e6f0fe 2015-08-13 05:09:44.422 UTC 00024fec-5f2d-4438-a0e2-d22418eaf89c 2015-08-13 03:37:43.142 UTC 217961e4-d3f5-4c89-8a2a-fb3fdb0c7f8f 2015-08-20 22:51:09.911 UTC 3f519bf0-8dd7-40e9-b680-46a0d00670e1 2015-08-13 03:59:22.665 UTC 4816d0fe-e2df-4c5f-95a1-4cedfb0bcc48 2015-08-13 05:01:58.22 UTC d517742d-d62d-47e3-beb8-8001d1c2c8a8 2015-08-15 01:24:13.479 UTC 8c24432c-c183-462c-a366-c6883eb637c2 2015-08-13 03:51:49.609 UTC 8f6961bb-a05a-4082-88f1-a55e09649d86 2015-08-15 01:28:52.401 UTC 7ef3f44c-ad80-422b-8fe9-36578375a3af 2015-08-13 03:43:12.391 UTC 417084ca-34c6-4db2-97dc-3f89557f7c14 2015-08-13 04:34:16.493 UTC eff75edd-b6ef-407b-ab48-566aebb2f4b2 2015-08-13 04:22:08.700 UTC bc36ef81-e814-4ee3-8421-2b8f1827b3d8 2015-08-13 03:54:18.780 UTC 214bd978-8da5-4f7a-86f1-96808fb3d15c 2015-08-18 20:59:49.906 UTC 5c9aa4b8-43b9-46bc-9fd1-e2959cf7ab2d 2015-08-18 19:57:19.901 UTC 9cc841a3-cdd8-4ecd-918c-0ff3b71a31d6 2015-08-13 02:41:37.297 UTC 3e2b1963-cbd7-4a09-9eda-9bf482f4f456 2015-08-18 19:48:07.104 UTC f50cd8c2-114f-4789-b61b-7c5bea10eb0c 2015-08-15 01:02:03.407 UTC 080a493f-0de5-47e0-aea4-c3625878d75e 2015-08-14 23:55:44.738 UTC