taverna-t2flow 0.2.0 → 0.3.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (26) hide show
  1. data/CHANGES.rdoc +16 -0
  2. data/README.rdoc +30 -21
  3. data/Rakefile +54 -0
  4. data/lib/t2flow/model.rb +7 -0
  5. data/lib/t2flow/parser.rb +7 -2
  6. data/taverna-t2flow.gemspec +76 -0
  7. data/test/fixtures/1000.t2flow +244 -0
  8. data/test/fixtures/1001.t2flow +321 -0
  9. data/test/fixtures/1002.t2flow +474 -0
  10. data/test/fixtures/1003.t2flow +292 -0
  11. data/test/fixtures/1004.t2flow +73 -0
  12. data/test/fixtures/996.t2flow +193 -0
  13. data/test/fixtures/997.t2flow +359 -0
  14. data/test/fixtures/998.t2flow +324 -0
  15. data/test/fixtures/999.t2flow +604 -0
  16. data/test/fixtures/basic.t2flow +94 -0
  17. data/test/fixtures/coordinated.t2flow +63 -0
  18. data/test/fixtures/linked.t2flow +88 -0
  19. data/test/fixtures/nested.t2flow +270 -0
  20. data/test/fixtures/processors.t2flow +174 -0
  21. data/test/run_tests.rb +7 -0
  22. data/test/test_bogus_workflows.rb +80 -0
  23. data/test/test_helper.rb +50 -0
  24. data/test/test_starter_pack_workflows.rb +132 -0
  25. metadata +121 -69
  26. data/ChangeLog.rdoc +0 -7
data/test/fixtures/996.t2flow ADDED
@@ -0,0 +1,193 @@
1
+ <workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.1.0"><dataflow id="0e367ee5-b4fa-4e61-91f6-f3b976d07921" role="top"><name>A_workflow_version_of_the_EMBOSS_tutorial</name><inputPorts /><outputPorts><port><name>outputPlot</name><annotations /></port><port><name>tmapPlot</name><annotations /></port><port><name>prophetOutput</name><annotations /></port></outputPorts><processors><processor><name>sequenceid</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
2
+ <value>swallid:ops2_*</value>
3
+ </net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
4
+ <maxJobs>1</maxJobs>
5
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
6
+ <backoffFactor>1.0</backoffFactor>
7
+ <initialDelay>1000</initialDelay>
8
+ <maxDelay>5000</maxDelay>
9
+ <maxRetries>0</maxRetries>
10
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>msfFormat</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
11
+ <value>msf</value>
12
+ </net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
13
+ <maxJobs>1</maxJobs>
14
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
15
+ <backoffFactor>1.0</backoffFactor>
16
+ <initialDelay>1000</initialDelay>
17
+ <maxDelay>5000</maxDelay>
18
+ <maxRetries>0</maxRetries>
19
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>send</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
20
+ <value>1171</value>
21
+ </net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
22
+ <maxJobs>1</maxJobs>
23
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
24
+ <backoffFactor>1.0</backoffFactor>
25
+ <initialDelay>1000</initialDelay>
26
+ <maxDelay>5000</maxDelay>
27
+ <maxRetries>0</maxRetries>
28
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>sbegin</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
29
+ <value>110</value>
30
+ </net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
31
+ <maxJobs>1</maxJobs>
32
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
33
+ <backoffFactor>1.0</backoffFactor>
34
+ <initialDelay>1000</initialDelay>
35
+ <maxDelay>5000</maxDelay>
36
+ <maxRetries>0</maxRetries>
37
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>transeqSequenceID</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
38
+ <value>embl:xlrhodop</value>
39
+ </net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
40
+ <maxJobs>1</maxJobs>
41
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
42
+ <backoffFactor>1.0</backoffFactor>
43
+ <initialDelay>1000</initialDelay>
44
+ <maxDelay>5000</maxDelay>
45
+ <maxRetries>0</maxRetries>
46
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>prophecyName</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
47
+ <value>Ops2 Sequences</value>
48
+ </net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
49
+ <maxJobs>1</maxJobs>
50
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
51
+ <backoffFactor>1.0</backoffFactor>
52
+ <initialDelay>1000</initialDelay>
53
+ <maxDelay>5000</maxDelay>
54
+ <maxRetries>0</maxRetries>
55
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>prophecyType</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
56
+ <value>G</value>
57
+ </net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
58
+ <maxJobs>1</maxJobs>
59
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
60
+ <backoffFactor>1.0</backoffFactor>
61
+ <initialDelay>1000</initialDelay>
62
+ <maxDelay>5000</maxDelay>
63
+ <maxRetries>0</maxRetries>
64
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy /></iteration></iterationStrategyStack></processor><processor><name>seqret</name><inputPorts><port><name>sequence_usa</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outseq</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>soaplab-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.soaplab.SoaplabActivity</class><inputMap><map from="sequence_usa" to="sequence_usa" /></inputMap><outputMap><map from="outseq" to="outseq" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
65
+ <endpoint>http://www.ebi.ac.uk/soaplab/emboss4/services/edit.seqret</endpoint>
66
+ <pollingInterval>0</pollingInterval>
67
+ <pollingBackoff>1.0</pollingBackoff>
68
+ <pollingIntervalMax>0</pollingIntervalMax>
69
+ </net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
70
+ <maxJobs>1</maxJobs>
71
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
72
+ <backoffFactor>1.0</backoffFactor>
73
+ <initialDelay>1000</initialDelay>
74
+ <maxDelay>5000</maxDelay>
75
+ <maxRetries>0</maxRetries>
76
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="sequence_usa" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>formatSequences</name><inputPorts><port><name>sequence_direct_data</name><depth>0</depth></port><port><name>osformat</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outseq</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>soaplab-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.soaplab.SoaplabActivity</class><inputMap><map from="sequence_direct_data" to="sequence_direct_data" /><map from="osformat" to="osformat" /></inputMap><outputMap><map from="outseq" to="outseq" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
77
+ <endpoint>http://www.ebi.ac.uk/soaplab/emboss4/services/edit.seqret</endpoint>
78
+ <pollingInterval>0</pollingInterval>
79
+ <pollingBackoff>1.0</pollingBackoff>
80
+ <pollingIntervalMax>0</pollingIntervalMax>
81
+ </net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
82
+ <maxJobs>1</maxJobs>
83
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
84
+ <backoffFactor>1.0</backoffFactor>
85
+ <initialDelay>1000</initialDelay>
86
+ <maxDelay>5000</maxDelay>
87
+ <maxRetries>0</maxRetries>
88
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="sequence_direct_data" depth="0" /><port name="osformat" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>emma</name><inputPorts><port><name>sequence_direct_data</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outseq</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>soaplab-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.soaplab.SoaplabActivity</class><inputMap><map from="sequence_direct_data" to="sequence_direct_data" /></inputMap><outputMap><map from="outseq" to="outseq" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
89
+ <endpoint>http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_multiple.emma</endpoint>
90
+ <pollingInterval>0</pollingInterval>
91
+ <pollingBackoff>1.0</pollingBackoff>
92
+ <pollingIntervalMax>0</pollingIntervalMax>
93
+ </net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
94
+ <maxJobs>1</maxJobs>
95
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
96
+ <backoffFactor>1.0</backoffFactor>
97
+ <initialDelay>1000</initialDelay>
98
+ <maxDelay>5000</maxDelay>
99
+ <maxRetries>0</maxRetries>
100
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="sequence_direct_data" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>prettyplot</name><inputPorts><port><name>sequences_direct_data</name><depth>0</depth></port></inputPorts><outputPorts><port><name>Graphics_in_PNG</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>soaplab-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.soaplab.SoaplabActivity</class><inputMap><map from="sequences_direct_data" to="sequences_direct_data" /></inputMap><outputMap><map from="Graphics_in_PNG" to="Graphics_in_PNG" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
101
+ <endpoint>http://www.ebi.ac.uk/soaplab/emboss4/services/display.prettyplot</endpoint>
102
+ <pollingInterval>0</pollingInterval>
103
+ <pollingBackoff>1.0</pollingBackoff>
104
+ <pollingIntervalMax>0</pollingIntervalMax>
105
+ </net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
106
+ <maxJobs>1</maxJobs>
107
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
108
+ <backoffFactor>1.0</backoffFactor>
109
+ <initialDelay>1000</initialDelay>
110
+ <maxDelay>5000</maxDelay>
111
+ <maxRetries>0</maxRetries>
112
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="sequences_direct_data" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>tmap</name><inputPorts><port><name>sequences_direct_data</name><depth>0</depth></port></inputPorts><outputPorts><port><name>Graphics_in_PNG</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>soaplab-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.soaplab.SoaplabActivity</class><inputMap><map from="sequences_direct_data" to="sequences_direct_data" /></inputMap><outputMap><map from="Graphics_in_PNG" to="Graphics_in_PNG" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
113
+ <endpoint>http://www.ebi.ac.uk/soaplab/emboss4/services/protein_2d_structure.tmap</endpoint>
114
+ <pollingInterval>0</pollingInterval>
115
+ <pollingBackoff>1.0</pollingBackoff>
116
+ <pollingIntervalMax>0</pollingIntervalMax>
117
+ </net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
118
+ <maxJobs>1</maxJobs>
119
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
120
+ <backoffFactor>1.0</backoffFactor>
121
+ <initialDelay>1000</initialDelay>
122
+ <maxDelay>5000</maxDelay>
123
+ <maxRetries>0</maxRetries>
124
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="sequences_direct_data" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>transeq</name><inputPorts><port><name>send</name><depth>0</depth></port><port><name>sbegin</name><depth>0</depth></port><port><name>sequence_usa</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outseq</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>soaplab-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.soaplab.SoaplabActivity</class><inputMap><map from="send" to="send" /><map from="sbegin" to="sbegin" /><map from="sequence_usa" to="sequence_usa" /></inputMap><outputMap><map from="outseq" to="outseq" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
125
+ <endpoint>http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_translation.transeq</endpoint>
126
+ <pollingInterval>0</pollingInterval>
127
+ <pollingBackoff>1.0</pollingBackoff>
128
+ <pollingIntervalMax>0</pollingIntervalMax>
129
+ </net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
130
+ <maxJobs>1</maxJobs>
131
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
132
+ <backoffFactor>1.0</backoffFactor>
133
+ <initialDelay>1000</initialDelay>
134
+ <maxDelay>5000</maxDelay>
135
+ <maxRetries>0</maxRetries>
136
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="send" depth="0" /><port name="sbegin" depth="0" /><port name="sequence_usa" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>prophecy</name><inputPorts><port><name>name</name><depth>0</depth></port><port><name>type</name><depth>0</depth></port><port><name>sequence_direct_data</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outfile</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>soaplab-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.soaplab.SoaplabActivity</class><inputMap><map from="sequence_direct_data" to="sequence_direct_data" /><map from="name" to="name" /><map from="type" to="type" /></inputMap><outputMap><map from="outfile" to="outfile" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
137
+ <endpoint>http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_profiles.prophecy</endpoint>
138
+ <pollingInterval>0</pollingInterval>
139
+ <pollingBackoff>1.0</pollingBackoff>
140
+ <pollingIntervalMax>0</pollingIntervalMax>
141
+ </net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
142
+ <maxJobs>1</maxJobs>
143
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
144
+ <backoffFactor>1.0</backoffFactor>
145
+ <initialDelay>1000</initialDelay>
146
+ <maxDelay>5000</maxDelay>
147
+ <maxRetries>0</maxRetries>
148
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="name" depth="0" /><port name="type" depth="0" /><port name="sequence_direct_data" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>prophet</name><inputPorts><port><name>infile_direct_data</name><depth>0</depth></port><port><name>sequence_direct_data</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outfile</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>soaplab-activity</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.activities.soaplab.SoaplabActivity</class><inputMap><map from="sequence_direct_data" to="sequence_direct_data" /><map from="infile_direct_data" to="infile_direct_data" /></inputMap><outputMap><map from="outfile" to="outfile" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean xmlns="">
149
+ <endpoint>http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_profiles.prophet</endpoint>
150
+ <pollingInterval>0</pollingInterval>
151
+ <pollingBackoff>1.0</pollingBackoff>
152
+ <pollingIntervalMax>0</pollingIntervalMax>
153
+ </net.sf.taverna.t2.activities.soaplab.SoaplabActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
154
+ <maxJobs>1</maxJobs>
155
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
156
+ <backoffFactor>1.0</backoffFactor>
157
+ <initialDelay>1000</initialDelay>
158
+ <maxDelay>5000</maxDelay>
159
+ <maxRetries>0</maxRetries>
160
+ </net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.0</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="infile_direct_data" depth="0" /><port name="sequence_direct_data" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>seqret</processor><port>sequence_usa</port></sink><source type="processor"><processor>sequenceid</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>formatSequences</processor><port>sequence_direct_data</port></sink><source type="processor"><processor>seqret</processor><port>outseq</port></source></datalink><datalink><sink type="processor"><processor>formatSequences</processor><port>osformat</port></sink><source type="processor"><processor>msfFormat</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>emma</processor><port>sequence_direct_data</port></sink><source type="processor"><processor>seqret</processor><port>outseq</port></source></datalink><datalink><sink type="processor"><processor>prettyplot</processor><port>sequences_direct_data</port></sink><source type="processor"><processor>emma</processor><port>outseq</port></source></datalink><datalink><sink type="processor"><processor>tmap</processor><port>sequences_direct_data</port></sink><source type="processor"><processor>formatSequences</processor><port>outseq</port></source></datalink><datalink><sink type="processor"><processor>transeq</processor><port>send</port></sink><source type="processor"><processor>send</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>transeq</processor><port>sbegin</port></sink><source type="processor"><processor>sbegin</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>transeq</processor><port>sequence_usa</port></sink><source type="processor"><processor>transeqSequenceID</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>prophecy</processor><port>name</port></sink><source type="processor"><processor>prophecyName</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>prophecy</processor><port>type</port></sink><source type="processor"><processor>prophecyType</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>prophecy</processor><port>sequence_direct_data</port></sink><source type="processor"><processor>emma</processor><port>outseq</port></source></datalink><datalink><sink type="processor"><processor>prophet</processor><port>infile_direct_data</port></sink><source type="processor"><processor>prophecy</processor><port>outfile</port></source></datalink><datalink><sink type="processor"><processor>prophet</processor><port>sequence_direct_data</port></sink><source type="processor"><processor>transeq</processor><port>outseq</port></source></datalink><datalink><sink type="dataflow"><port>outputPlot</port></sink><source type="processor"><processor>prettyplot</processor><port>Graphics_in_PNG</port></source></datalink><datalink><sink type="dataflow"><port>tmapPlot</port></sink><source type="processor"><processor>tmap</processor><port>Graphics_in_PNG</port></source></datalink><datalink><sink type="dataflow"><port>prophetOutput</port></sink><source type="processor"><processor>prophet</processor><port>outfile</port></source></datalink></datalinks><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
161
+ <annotationAssertions>
162
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
163
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
164
+ <text>Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.</text>
165
+ </annotationBean>
166
+ <date>2009-12-15 20:15:31.62 GMT</date>
167
+ <creators />
168
+ <curationEventList />
169
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
170
+ </annotationAssertions>
171
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
172
+ <annotationAssertions>
173
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
174
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
175
+ <text>A workflow version of the EMBOSS tutorial</text>
176
+ </annotationBean>
177
+ <date>2009-12-15 20:15:12.279 GMT</date>
178
+ <creators />
179
+ <curationEventList />
180
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
181
+ </annotationAssertions>
182
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
183
+ <annotationAssertions>
184
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
185
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
186
+ <text>Tom Oinn</text>
187
+ </annotationBean>
188
+ <date>2009-12-15 20:15:02.217 GMT</date>
189
+ <creators />
190
+ <curationEventList />
191
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
192
+ </annotationAssertions>
193
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>