Workflow Entry: Nucleotide frequency workflow

Created at: 13/05/10 @ 01:51:22 Last updated: 12/11/10 @ 10:30:15

Version 2 (latest) (of 2)

Version created on: 12/11/10 @ 10:30:12 by: wabi | Revision comments Expand

Title: Nucleotide frequency workflow

Type: Taverna 2

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Workflow Components

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Titles (1)

Descriptions (0)

Inputs (3)

Name	Description
gene_name
function
email

Processors (28)

Name	Type	Description
Make_query_for_searching_DDBJ	beanshell
Get_DDBJ_list_by_ARSA_searchByXMLPath	localworker
Split_string_DDBJ_list_by_enter	localworker
Split_string_enter	stringconstant
Skip_first_two_lines	beanshell
Split_string_tab	stringconstant
Split_string_DDBJ_list_lines_by_tab	localworker
Make_query_for_searching_DDBJ_to_get_feature_info	beanshell
Get_variation_information_by_DDBJ_get	localworker
Split_string_variation_information_by_enter	localworker
Summarize_variation_information	beanshell
Split_string_variation_information_lines_by_tab	localworker
Make_output_for_DDBJ	beanshell
Make_query_for_searching_dbsnp_by_esearch	beanshell
Get_dbsnp_list_by_ncbieutils_esearch	localworker
Make_query_for_searching_dbsnp_by_efetch	beanshell
Split_string_dbsnp_list_by_enter	localworker
Get_dbsnp_summary_by_ncbieutils_efetch	localworker
Extract_not_merged_rsid	beanshell
Make_query_for_retrieving_genotype	beanshell
Get_dbsnp_genotype_frequency_by_ncbieutils_efetch	localworker
Extraction_of_genotype_and_frequency_of_each_population	beanshell
Make_query_for_searching_pubmed	beanshell
Get_dbsnp_pubmed_cited_by_ncbieutils_elink	localworker
Summarize_cited_snp	beanshell
Merge_output	beanshell
Extract_pubmed_id	beanshell
Split_string_dbsnp_summary_by_enter	localworker

Beanshells (14)

Name	Inputs	Outputs
Make_query_for_searching_DDBJ	gene	url
Skip_first_two_lines	list	ddbjList
Make_query_for_searching_DDBJ_to_get_feature_info	ddbjList	urlList
Summarize_variation_information	list	variationAnnotation
Make_output_for_DDBJ	ddbj variation	output
Make_query_for_searching_dbsnp_by_esearch	function gene email	url param
Make_query_for_searching_dbsnp_by_efetch	result email	urlList
Extract_not_merged_rsid	dbsnpEfetchResultList	notMergedRsidList
Make_query_for_retrieving_genotype	rsId email	url
Extraction_of_genotype_and_frequency_of_each_population	inputList rsIdList	output
Make_query_for_searching_pubmed	rsId email	url id
Summarize_cited_snp	pubmedIdList rsId	output
Merge_output	ddbj genotypeInfo citedPaper	output
Extract_pubmed_id	elinkResult	pubmedIdList

Outputs (1)

Name	Description
Nucleotide_frequency

Datalinks (43)

Source	Sink
gene_name	Make_query_for_searching_DDBJ:gene
Make_query_for_searching_DDBJ:url	Get_DDBJ_list_by_ARSA_searchByXMLPath:url
Get_DDBJ_list_by_ARSA_searchByXMLPath:contents	Split_string_DDBJ_list_by_enter:string
Split_string_enter:value	Split_string_DDBJ_list_by_enter:regex
Split_string_DDBJ_list_lines_by_tab:split	Skip_first_two_lines:list
Split_string_DDBJ_list_by_enter:split	Split_string_DDBJ_list_lines_by_tab:string
Split_string_tab:value	Split_string_DDBJ_list_lines_by_tab:regex
Skip_first_two_lines:ddbjList	Make_query_for_searching_DDBJ_to_get_feature_info:ddbjList
Make_query_for_searching_DDBJ_to_get_feature_info:urlList	Get_variation_information_by_DDBJ_get:url
Get_variation_information_by_DDBJ_get:contents	Split_string_variation_information_by_enter:string
Split_string_enter:value	Split_string_variation_information_by_enter:regex
Split_string_variation_information_lines_by_tab:split	Summarize_variation_information:list
Split_string_variation_information_by_enter:split	Split_string_variation_information_lines_by_tab:string
Split_string_tab:value	Split_string_variation_information_lines_by_tab:regex
Skip_first_two_lines:ddbjList	Make_output_for_DDBJ:ddbj
Summarize_variation_information:variationAnnotation	Make_output_for_DDBJ:variation
email	Make_query_for_searching_dbsnp_by_esearch:email
function	Make_query_for_searching_dbsnp_by_esearch:function
gene_name	Make_query_for_searching_dbsnp_by_esearch:gene
Make_query_for_searching_dbsnp_by_esearch:url	Get_dbsnp_list_by_ncbieutils_esearch:url
Split_string_dbsnp_list_by_enter:split	Make_query_for_searching_dbsnp_by_efetch:result
email	Make_query_for_searching_dbsnp_by_efetch:email
Get_dbsnp_list_by_ncbieutils_esearch:contents	Split_string_dbsnp_list_by_enter:string
Split_string_enter:value	Split_string_dbsnp_list_by_enter:regex
Make_query_for_searching_dbsnp_by_efetch:urlList	Get_dbsnp_summary_by_ncbieutils_efetch:url
Split_string_dbsnp_summary_by_enter:split	Extract_not_merged_rsid:dbsnpEfetchResultList
Extract_not_merged_rsid:notMergedRsidList	Make_query_for_retrieving_genotype:rsId
email	Make_query_for_retrieving_genotype:email
Make_query_for_retrieving_genotype:url	Get_dbsnp_genotype_frequency_by_ncbieutils_efetch:url
Get_dbsnp_genotype_frequency_by_ncbieutils_efetch:contents	Extraction_of_genotype_and_frequency_of_each_population:inputList
Extract_not_merged_rsid:notMergedRsidList	Extraction_of_genotype_and_frequency_of_each_population:rsIdList
email	Make_query_for_searching_pubmed:email
Extract_not_merged_rsid:notMergedRsidList	Make_query_for_searching_pubmed:rsId
Make_query_for_searching_pubmed:url	Get_dbsnp_pubmed_cited_by_ncbieutils_elink:url
Extract_pubmed_id:pubmedIdList	Summarize_cited_snp:pubmedIdList
Make_query_for_searching_pubmed:id	Summarize_cited_snp:rsId
Summarize_cited_snp:output	Merge_output:citedPaper
Make_output_for_DDBJ:output	Merge_output:ddbj
Extraction_of_genotype_and_frequency_of_each_population:output	Merge_output:genotypeInfo
Get_dbsnp_pubmed_cited_by_ncbieutils_elink:contents	Extract_pubmed_id:elinkResult
Split_string_enter:value	Split_string_dbsnp_summary_by_enter:regex
Get_dbsnp_summary_by_ncbieutils_efetch:contents	Split_string_dbsnp_summary_by_enter:string
Merge_output:output	Nucleotide_frequency

Coordinations (8)

Controller	Target
Summarize_variation_information	Make_output_for_DDBJ
Skip_first_two_lines	Make_output_for_DDBJ
Extract_pubmed_id	Summarize_cited_snp
Split_string_dbsnp_summary_by_enter	Extract_not_merged_rsid
Extraction_of_genotype_and_frequency_of_each_population	Merge_output
Summarize_cited_snp	Merge_output
Get_dbsnp_genotype_frequency_by_ncbieutils_efetch	Extraction_of_genotype_and_frequency_of_each_population
Make_output_for_DDBJ	Merge_output