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_2.xml
Created: 2008-07-12 09:15:13
Last updated: 2008-07-12 20:20:52
No description has been set
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Workflow Components
Processors (23)
| Name |
Type |
Description |
| species |
stringconstant |
|
| end |
stringconstant |
|
| regex |
stringconstant |
|
| split_by_regex |
local |
|
| getGeneInfo |
arbitrarywsdl |
get gene information |
| parse_swiss |
beanshell |
|
| remove_Nulls |
beanshell |
|
| start |
stringconstant |
|
| chromo |
stringconstant |
|
| options |
stringconstant |
|
| add_uniprot_to_string |
beanshell |
|
| merge_swissprot |
local |
|
| split_uniprot_strings |
local |
|
| Kegg_gene_ids |
arbitrarywsdl |
|
| merge_pathways |
local |
|
| getgenesbyspecies |
soaplabwsdl |
Retrieves a list of Ensembl genes for a given species, chromosome and position |
| parse_ddbj_gene_info |
soaplabwsdl |
extract information from geneGeneInfo processor at http://xml.nig.ac.jp/wsdl/Ensembl.wsdl |
| getcurrentdatabase |
soaplabwsdl |
Retrieves the current databases from ENSEMBL for a species |
| get_pathways_by_genes |
arbitrarywsdl |
|
| parse_gene_id |
beanshell |
|
| merge_gene_ids |
local |
|
| remove_nulls_2 |
beanshell |
|
| lister |
arbitrarywsdl |
|
Beanshells (5)
| Name |
Description |
Inputs |
Outputs |
| parse_swiss |
|
input
|
output
|
| remove_Nulls |
|
input
|
output
|
| add_uniprot_to_string |
|
input
|
output
|
| parse_gene_id |
|
input
|
output
|
| remove_nulls_2 |
|
input
|
output
|
Outputs (2)
| Name |
Description |
| merged_kegg_pathways |
|
| genes_in_qtl |
|
Links (25)
| Source |
Sink |
| Kegg_gene_ids:return |
merge_gene_ids:stringlist |
| add_uniprot_to_string:output |
split_uniprot_strings: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 |
split_by_regex:string |
| lister:listerReturn |
get_pathways_by_genes:genes_id_list |
| merge_gene_ids:concatenated |
remove_nulls_2:input |
| merge_swissprot:concatenated |
remove_Nulls:input |
| options:value |
parse_ddbj_gene_info:options |
| parse_ddbj_gene_info:output |
parse_swiss:input |
| parse_gene_id:output |
lister:file |
| parse_swiss:output |
merge_swissprot:stringlist |
| regex:value |
split_by_regex:regex |
| regex:value |
split_uniprot_strings:regex |
| remove_Nulls:output |
add_uniprot_to_string:input |
| remove_nulls_2:output |
parse_gene_id:input |
| getgenesbyspecies:output |
genes_in_qtl |
| merge_pathways:concatenated |
merged_kegg_pathways |
| species:value |
getcurrentdatabase:species |
| split_by_regex:split |
getGeneInfo:geneId |
| split_uniprot_strings:split |
Kegg_gene_ids:string |
| start:value |
getgenesbyspecies:start |
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