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.
qtl_pathway_3.xml
Created: 2008-07-12 09:10:15
Last updated: 2008-07-12 11:44:53
No description has been set
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Workflow Components
Processors (24)
| Name |
Type |
Description |
| species |
stringconstant |
|
| start |
stringconstant |
|
| regex |
stringconstant |
|
| end |
stringconstant |
|
| remove_Nulls |
beanshell |
|
| add_uniproti_to_string |
beanshell |
|
| parse_swiss |
beanshell |
|
| options |
stringconstant |
|
| chromo |
stringconstant |
|
| split_by_regex |
local |
|
| getGeneInfo |
arbitrarywsdl |
get gene information |
| split_gene_ids |
beanshell |
|
| Kegg_gene_ids |
arbitrarywsdl |
|
| 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 |
| getgenesbyspecies |
soaplabwsdl |
Retrieves a list of Ensembl genes for a given species, chromosome and position |
| Split_string_into_string_list_by_regular_expression |
local |
|
| regex_2 |
stringconstant |
|
| NestedWorkflow |
workflow |
|
| merge_swiss_ids |
local |
|
| merge_genes_and_pathways |
local |
|
| btit |
arbitrarywsdl |
|
| Concatenate_two_strings |
local |
|
| Merge_string_list_to_string |
local |
|
Beanshells (4)
| Name |
Description |
Inputs |
Outputs |
| remove_Nulls |
|
input
|
output
|
| add_uniproti_to_string |
|
input
|
output
|
| parse_swiss |
|
input
|
output
|
| split_gene_ids |
|
input
|
output
|
Outputs (6)
| Name |
Description |
| genes_in_qtl |
|
| pathway_genes |
|
| pathway_output |
|
| complete_merged |
|
| kegg_definitions |
|
| merged_definitions |
|
Links (30)
| Source |
Sink |
| Concatenate_two_strings:output |
Merge_string_list_to_string:stringlist |
| Concatenate_two_strings:output |
kegg_definitions |
| Kegg_gene_ids:return |
split_gene_ids:input |
| Merge_string_list_to_string:concatenated |
merged_definitions |
| NestedWorkflow:pathway_genes |
merge_genes_and_pathways:stringlist |
| Split_string_into_string_list_by_regular_expression:split |
Concatenate_two_strings:string1 |
| Split_string_into_string_list_by_regular_expression:split |
NestedWorkflow:gene_ids |
| Split_string_into_string_list_by_regular_expression:split |
btit:string |
| add_uniproti_to_string:output |
Kegg_gene_ids:string |
| btit:return |
Concatenate_two_strings:string2 |
| chromo:value |
getgenesbyspecies:chromo |
| end:value |
getgenesbyspecies:end |
| getGeneInfo:Result |
parse_ddbj_gene_info:file_direct_data |
| getcurrentdatabase:output |
getgenesbyspecies:database |
| getgenesbyspecies:output |
split_by_regex:string |
| merge_genes_and_pathways:concatenated |
complete_merged |
| merge_swiss_ids:concatenated |
remove_Nulls:input |
| options:value |
parse_ddbj_gene_info:options |
| parse_ddbj_gene_info:output |
parse_swiss:input |
| parse_swiss:output |
merge_swiss_ids:stringlist |
| NestedWorkflow:pathway_genes |
pathway_genes |
| NestedWorkflow:pathway_output |
pathway_output |
| regex:value |
split_by_regex:regex |
| regex_2:value |
Split_string_into_string_list_by_regular_expression:regex |
| remove_Nulls:output |
add_uniproti_to_string:input |
| species:value |
getcurrentdatabase:species |
| split_by_regex:split |
getGeneInfo:geneId |
| split_gene_ids:output |
Split_string_into_string_list_by_regular_expression:string |
| start:value |
getgenesbyspecies:start |
| getgenesbyspecies:output |
genes_in_qtl |
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