Workflow Entry: Virus genome extraction workflow
Created at: 13/05/10 @ 01:59:19
Last updated: 13/05/10 @ 01:59:48
Version 1
(of 1)
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Title:
Virus genome extraction workflow
Type:
Taverna 2
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Description
Retrieve genome entries which agree with the following conditions regarding the Definition item of entries from both VRL and PHG division in DDBJ.
- Includes "complete sequence" or includes "segment" and "complete sequence"
- Not include "TPA:" and "nearly complete"
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Workflow Components
![header=[] body=[This is the author information extracted from the workflow version] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1202402239)
Authors (0)
![header=[] body=[These are the descriptive titles embedded within the workflow version] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1202402239)
Titles (2)
| Virus genome extraction workflow |
| Retrieving virus entry workflow |
![header=[] body=[These are the descriptions embedded within the workflow version] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1202402239)
Descriptions (0)
Processors (9)
| Name |
Type |
Description |
| Make_query_for_retrieving_hitcount_of_virus_genome_entry_from_DDBJ |
beanshell |
|
| Get_DDBJ_list_by_ARSA_searchByXMLPath |
localworker |
|
| Split_string_DDBJ_list_by_enter |
localworker |
|
| Split_string_enter |
stringconstant |
|
| Get_HitCount |
beanshell |
|
| Make_Offsets |
beanshell |
|
| Make_query_for_retrieving_gene_type |
beanshell |
|
| Get_gene_type_by_ARSA_searchByXMLPath |
localworker |
|
| Print_virus_genome_entries |
beanshell |
|
Beanshells (5)
| Name |
Description |
Inputs |
Outputs |
| Make_query_for_retrieving_hitcount_of_virus_genome_entry_from_DDBJ |
|
|
query
|
| Get_HitCount |
|
arsaResult
|
arsaResultNum
|
| Make_Offsets |
|
hitCount
|
offsets
|
| Make_query_for_retrieving_gene_type |
|
offsets
|
queries
|
| Print_virus_genome_entries |
|
ARSA_results
arsaResultNum
|
retrieving_virus_entry
|
Outputs (1)
| Name |
Description |
| Virus_genome_entry |
|
Datalinks (10)
| Source |
Sink |
| Make_query_for_retrieving_hitcount_of_virus_genome_entry_from_DDBJ:query |
Get_DDBJ_list_by_ARSA_searchByXMLPath:url |
| Split_string_enter:value |
Split_string_DDBJ_list_by_enter:regex |
| Get_DDBJ_list_by_ARSA_searchByXMLPath:contents |
Split_string_DDBJ_list_by_enter:string |
| Split_string_DDBJ_list_by_enter:split |
Get_HitCount:arsaResult |
| Get_HitCount:arsaResultNum |
Make_Offsets:hitCount |
| Make_Offsets:offsets |
Make_query_for_retrieving_gene_type:offsets |
| Make_query_for_retrieving_gene_type:queries |
Get_gene_type_by_ARSA_searchByXMLPath:url |
| Get_gene_type_by_ARSA_searchByXMLPath:contents |
Print_virus_genome_entries:ARSA_results |
| Get_HitCount:arsaResultNum |
Print_virus_genome_entries:arsaResultNum |
| Print_virus_genome_entries:retrieving_virus_entry |
Virus_genome_entry |
Coordinations (1)
| Controller |
Target |
| Get_gene_type_by_ARSA_searchByXMLPath |
Print_virus_genome_entries |
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