Workflow Entry: complete_2.xml

Created at: 12/07/08 @ 09:44:05 Last updated: 12/07/08 @ 09:44:22

Version 1 (of 1)

Version created on: 12/07/08 @ 09:44:05 by: Antoon Goderis | Revision comments Expand

Last edited on: 12/07/08 @ 09:44:22 by: Antoon Goderis

Title: complete_2.xml

Type: Taverna 1

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Description

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Workflow Components

Inputs (0)

Processors (24)

Name	Type	Description
end	stringconstant
regex1	stringconstant
regex_2	stringconstant
merge_string_list	local
chromosome	stringconstant
split_by_regex_2	local
merge_list_2	local
species	stringconstant
array_name	stringconstant
comma	stringconstant
start	stringconstant
split_by_regex	local
split_by_regex_3	local
Ensembl_gene_info	workflow
Remove_duplicates	workflow
getcurrentdatabase	soaplabwsdl	Retrieves the current databases from ENSEMBL for a species
Uniprot_record_search	workflow
getgenesbyspecies	soaplabwsdl	Retrieves a list of Ensembl genes for a given species, chromosome and position
Probesets_to_genes	workflow
Parse_gene_name	workflow
Parse_swiss_ids	workflow
Probeset_in_QTL	workflow
Remove_swiss_nulls	workflow
Remove_gene_nulls	workflow

Beanshells (4)

Name	Inputs	Outputs
parse_gene_info	input	output
parse_swiss	input	output
remove_Nulls	input	output
remove_Nulls	input	output

Outputs (8)

Name	Description
current_database
genes_in_region
gene_info
probesets_in_qtl
genes_from_probesets
swiss_prot
gene_name
uniprot_records

Links (40)

Source	Sink
Ensembl_gene_info:gene_info	Parse_gene_name:gene_info
Ensembl_gene_info:gene_info	Parse_swiss_ids:gene_info
Parse_gene_name:gene_name	Remove_gene_nulls:input_string
Parse_swiss_ids:swiss_ids	Remove_swiss_nulls:input_string
Probeset_in_QTL:probesets_in_qtl	split_by_regex:string
Probesets_to_genes:genes_from_probeset	Remove_duplicates:input_list_1
Remove_duplicates:unique_list	split_by_regex_3:string
Remove_swiss_nulls:removed_nulls	split_by_regex_2:string
Remove_gene_nulls:removed_nulls	gene_name
Uniprot_record_search:uniprot_record	merge_list_2:stringlist
array_name:value	Probeset_in_QTL:array_name
chromosome:value	Probeset_in_QTL:chromosome
chromosome:value	Probesets_to_genes:chromosome
chromosome:value	getgenesbyspecies:chromo
comma:value	merge_string_list:seperator
end:value	Probeset_in_QTL:end
end:value	Probesets_to_genes:end
end:value	getgenesbyspecies:end
getcurrentdatabase:output	Probeset_in_QTL:database
getcurrentdatabase:output	Probesets_to_genes:database
getcurrentdatabase:output	getgenesbyspecies:database
getgenesbyspecies:output	Remove_duplicates:input_list_2
Ensembl_gene_info:gene_info	gene_info
Parse_swiss_ids:swiss_ids	swiss_prot
Probeset_in_QTL:probesets_in_qtl	probesets_in_qtl
Probesets_to_genes:genes_from_probeset	genes_from_probesets
getcurrentdatabase:output	current_database
merge_list_2:concatenated	uniprot_records
merge_string_list:concatenated	Probesets_to_genes:probeset_list
regex1:value	split_by_regex:regex
regex_2:value	split_by_regex_2:regex
regex_2:value	split_by_regex_3:regex
species:value	getcurrentdatabase:species
split_by_regex:split	merge_string_list:stringlist
split_by_regex_2:split	Uniprot_record_search:swissprot_id
split_by_regex_3:split	Ensembl_gene_info:genes_in_region
start:value	Probeset_in_QTL:start
start:value	Probesets_to_genes:start
start:value	getgenesbyspecies:start
getgenesbyspecies:output	genes_in_region