This workflow uses one or more services that
are deprecated as of 31st December 2012
(almost 12 years ago), and may no longer function.
Show details...
Affected service WSDL:
- http://soap.genome.jp/KEGG.wsdl
Details:
KEGG will be moving from a WSDL/SOAP interface to REST. Details of the new REST services can be found here.
Working examples that use the new REST service can be viewed here, here and here.
unnested_qtl_pathway.xml
Created: 2008-07-12 09:12:44
Last updated: 2008-07-12 11:45:59
No description has been set
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Workflow Components
Processors (24)
Name |
Type |
Description |
start |
stringconstant |
|
merge_swissprot |
local |
|
regex |
stringconstant |
|
species |
stringconstant |
|
end |
stringconstant |
|
remove_Nulls |
beanshell |
|
add_ncbi_to_string |
beanshell |
|
merge_gene_pathways |
local |
|
chromo |
stringconstant |
|
merge_pathways_2 |
local |
|
options |
stringconstant |
|
parse_swiss |
beanshell |
|
merge_pathways |
local |
|
split_genes |
local |
|
split_by_regex |
local |
|
split_gene_ids |
beanshell |
|
Concatenate_two_strings |
local |
|
lister |
arbitrarywsdl |
|
get_pathways_by_genes |
arbitrarywsdl |
|
getcurrentdatabase |
soaplabwsdl |
Retrieves the current databases from ENSEMBL for a species |
parse_ddbj_gene_info |
soaplabwsdl |
extract information from geneGeneInfo processor at http://xml.nig.ac.jp/wsdl/Ensembl.wsdl |
getgenesbyspecies |
soaplabwsdl |
Retrieves a list of Ensembl genes for a given species, chromosome and position |
getGeneInfo |
arbitrarywsdl |
get gene information |
Kegg_gene_ids |
arbitrarywsdl |
|
Beanshells (4)
Name |
Description |
Inputs |
Outputs |
remove_Nulls |
|
input
|
output
|
add_ncbi_to_string |
|
input
|
output
|
parse_swiss |
|
input
|
output
|
split_gene_ids |
|
input
|
output
|
Outputs (3)
Name |
Description |
merged_kegg_pathways |
|
genes_in_qtl |
|
gene_and_pathway |
|
Links (28)
Source |
Sink |
Concatenate_two_strings:output |
merge_gene_pathways:stringlist |
Kegg_gene_ids:return |
split_gene_ids:input |
add_ncbi_to_string:output |
Kegg_gene_ids:string |
chromo:value |
getgenesbyspecies:chromo |
end:value |
getgenesbyspecies:end |
getGeneInfo:Result |
parse_ddbj_gene_info:file_direct_data |
get_pathways_by_genes:return |
merge_pathways:stringlist |
getcurrentdatabase:output |
getgenesbyspecies:database |
getgenesbyspecies:output |
genes_in_qtl |
getgenesbyspecies:output |
split_by_regex:string |
lister:attachmentList |
get_pathways_by_genes:genes_id_list |
merge_gene_pathways:concatenated |
gene_and_pathway |
merge_pathways:concatenated |
Concatenate_two_strings:string1 |
merge_pathways:concatenated |
merge_pathways_2:stringlist |
merge_pathways_2:concatenated |
merged_kegg_pathways |
merge_swissprot:concatenated |
remove_Nulls:input |
options:value |
parse_ddbj_gene_info:options |
parse_ddbj_gene_info:output |
parse_swiss:input |
parse_swiss:output |
merge_swissprot:stringlist |
regex:value |
split_by_regex:regex |
regex:value |
split_genes:regex |
remove_Nulls:output |
add_ncbi_to_string:input |
species:value |
getcurrentdatabase:species |
split_by_regex:split |
Concatenate_two_strings:string2 |
split_by_regex:split |
getGeneInfo:geneId |
split_gene_ids:output |
split_genes:string |
split_genes:split |
lister:file |
start:value |
getgenesbyspecies:start |
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licensed under:
Version 1
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