Oryza Sativa QTLs and genes retrieval from TropGene, Gramene and Ensembl

None

/default:methodResponse/default:return
/default:methodResponse/default:return
/default:methodResponse/default:return
List output=new LinkedList();
List qtl_id=new LinkedList();
for(int i=0;i11){
				if(end-start100){
					if(end-start
/default:methodResponse/default:return
/default:methodResponse/default:return
/default:methodResponse/default:return
/default:methodResponse/default:return
List output=new LinkedList();
List qtl_id=new LinkedList();
for(int i=0;i11){
				if(end-start100){
					if(end-start
List qtl_with_common_bps=new LinkedList();
List tropgene_position=new LinkedList();
List gramene_position=new LinkedList();
List chs=new LinkedList();
String chromosome="";
for(int i=0;igramene_start&&tropgene_stopgramene_stop){
			chs.add(chromosome);
			tropgene_position.add(Integer.valueOf(tropgene_start.intValue())+":"+Integer.valueOf(tropgene_stop.intValue()));			
			gramene_position.add(Integer.valueOf(gramene_start.intValue())+":"+Integer.valueOf(gramene_stop.intValue()));
		}
	}
}

Name	Description
Ontology_concept_term
max_qtl_size

Name	Type	Description
gramene_ontology_concept2identifier	wsdl	Wsdl http://gohelle.cirad.fr:8080/BioSemantic_webapp/services/get_medoc_gramene_marker_ontology_concept_term_identifier?wsdl Wsdl Operation method
gramene_ontology_concept2identifier_input	xmlsplitter
XPath_Service	xpath	Xpath Expression /default:methodResponse/default:return
gramene_identifier2sequence_position	wsdl	Wsdl http://gohelle.cirad.fr:8080/BioSemantic_webapp/services/get_medoc_gramene_marker_identifier_sequence_position?wsdl Wsdl Operation method
gramene_identifier2sequence_position_input	xmlsplitter
gramene_identifier2chromosome_name	wsdl	Wsdl http://gohelle.cirad.fr:8080/BioSemantic_webapp/services/get_medoc_gramene_marker_identifier_chromosome_name?wsdl Wsdl Operation method
gramene_identifier2chromosome_name_input	xmlsplitter
XPath_Service_4	xpath	Xpath Expression /default:methodResponse/default:return
XPath_Service_3	xpath	Xpath Expression /default:methodResponse/default:return
gramene_merge_chromosome_and_position	beanshell	Script List output=new LinkedList(); List qtl_id=new LinkedList(); for(int i=0;i11){ if(end-start100){ if(end-start
gramene_identifier2qtl_accession	wsdl	Wsdl http://gohelle.cirad.fr:8080/BioSemantic_webapp/services/get_medoc_gramene_marker_identifier_sequence_accession?wsdl Wsdl Operation method
gramene_identifier2qtl_accession_input	xmlsplitter
XPath_Service_2	xpath	Xpath Expression /default:methodResponse/default:return
osativa_eg_gene	biomart
tropgeneRice_ontology_concept_term2QTL	wsdl	Wsdl http://gohelle.cirad.fr:8080/BioSemantic_webapp/services/get_medoc_TROPGENE_RICE_ontology_concept_term_quantitative_trait_locus?wsdl Wsdl Operation method
tropgeneRice_ontology_concept_term2QTL_input	xmlsplitter
tropgeneRice_QTL2chromosome	wsdl	Wsdl http://gohelle.cirad.fr:8080/BioSemantic_webapp/services/get_medoc_TROPGENE_RICE_quantitative_trait_locus_chromosome_name?wsdl Wsdl Operation method
XPath_Service_5	xpath	Xpath Expression /default:methodResponse/default:return
XPath_Service_2_2	xpath	Xpath Expression /default:methodResponse/default:return
tropgeneRice_QTL2sequence_position	wsdl	Wsdl http://gohelle.cirad.fr:8080/BioSemantic_webapp/services/get_medoc_TROPGENE_RICE_quantitative_trait_locus_sequence_position?wsdl Wsdl Operation method
XPath_Service_4_2	xpath	Xpath Expression /default:methodResponse/default:return
tropgeneRice_QTL2chromosome_input	xmlsplitter
tropgeneRice_QTL2sequence_position_input	xmlsplitter
osativa_eg_gene_2	biomart
tropgene_merge_chromosome_and_position	beanshell	Script List output=new LinkedList(); List qtl_id=new LinkedList(); for(int i=0;i11){ if(end-start100){ if(end-start
qtl_with_common_positions	beanshell	Script List qtl_with_common_bps=new LinkedList(); List tropgene_position=new LinkedList(); List gramene_position=new LinkedList(); List chs=new LinkedList(); String chromosome=""; for(int i=0;igramene_start&&tropgene_stopgramene_stop){ chs.add(chromosome); tropgene_position.add(Integer.valueOf(tropgene_start.intValue())+":"+Integer.valueOf(tropgene_stop.intValue())); gramene_position.add(Integer.valueOf(gramene_start.intValue())+":"+Integer.valueOf(gramene_stop.intValue())); } } }

Name	Inputs	Outputs
gramene_merge_chromosome_and_position	positions_input chromosome_input max_qtl_size qtl_id_input	output qtl_id
tropgene_merge_chromosome_and_position	positions_input chromosome_input max_qtl_size qtl_id_input	output qtl_id
qtl_with_common_positions	gramene_data tropgene_data	chs tropgene_position gramene_position

Name	Description
qtl_accession_gramene
Ensembl_gene_gramene
Ensembl_gene_tropgene
qtl_accession_tropgene
common_qtl_position_gramene
common_qtl_position_tropgene
common_qtl_chromosome

Source	Sink
gramene_ontology_concept2identifier_input:output	gramene_ontology_concept2identifier:parameters
Ontology_concept_term	gramene_ontology_concept2identifier_input:input
gramene_ontology_concept2identifier:parameters	XPath_Service:xml_text
gramene_identifier2sequence_position_input:output	gramene_identifier2sequence_position:parameters
XPath_Service:nodelist	gramene_identifier2sequence_position_input:input
gramene_identifier2chromosome_name_input:output	gramene_identifier2chromosome_name:parameters
XPath_Service:nodelist	gramene_identifier2chromosome_name_input:input
gramene_identifier2chromosome_name:parameters	XPath_Service_4:xml_text
gramene_identifier2sequence_position:parameters	XPath_Service_3:xml_text
XPath_Service_3:nodelist	gramene_merge_chromosome_and_position:positions_input
XPath_Service_4:nodelist	gramene_merge_chromosome_and_position:chromosome_input
max_qtl_size	gramene_merge_chromosome_and_position:max_qtl_size
gramene_identifier2qtl_accession_input:output	gramene_identifier2qtl_accession:parameters
XPath_Service:nodelist	gramene_identifier2qtl_accession_input:input
gramene_identifier2qtl_accession:parameters	XPath_Service_2:xml_text
gramene_merge_chromosome_and_position:output	osativa_eg_gene:osativa_eg_gene.chromosomal_region_filter
tropgeneRice_ontology_concept_term2QTL_input:output	tropgeneRice_ontology_concept_term2QTL:parameters
Ontology_concept_term	tropgeneRice_ontology_concept_term2QTL_input:input
tropgeneRice_QTL2chromosome_input:output	tropgeneRice_QTL2chromosome:parameters
tropgeneRice_ontology_concept_term2QTL:parameters	XPath_Service_5:xml_text
tropgeneRice_QTL2chromosome:parameters	XPath_Service_2_2:xml_text
tropgeneRice_QTL2sequence_position_input:output	tropgeneRice_QTL2sequence_position:parameters
tropgeneRice_QTL2sequence_position:parameters	XPath_Service_4_2:xml_text
XPath_Service_5:nodelist	tropgeneRice_QTL2chromosome_input:input
XPath_Service_5:nodelist	tropgeneRice_QTL2sequence_position_input:input
tropgene_merge_chromosome_and_position:output	osativa_eg_gene_2:osativa_eg_gene.chromosomal_region_filter
XPath_Service_2_2:nodelist	tropgene_merge_chromosome_and_position:chromosome_input
XPath_Service_4_2:nodelist	tropgene_merge_chromosome_and_position:positions_input
max_qtl_size	tropgene_merge_chromosome_and_position:max_qtl_size
gramene_merge_chromosome_and_position:output	qtl_with_common_positions:gramene_data
tropgene_merge_chromosome_and_position:output	qtl_with_common_positions:tropgene_data
gramene_merge_chromosome_and_position:qtl_id	qtl_accession_gramene
osativa_eg_gene:osativa_eg_gene	Ensembl_gene_gramene
osativa_eg_gene_2:osativa_eg_gene	Ensembl_gene_tropgene
tropgene_merge_chromosome_and_position:qtl_id	qtl_accession_tropgene
qtl_with_common_positions:gramene_position	common_qtl_position_gramene
qtl_with_common_positions:tropgene_position	common_qtl_position_tropgene
qtl_with_common_positions:chs	common_qtl_chromosome

Oryza Sativa QTLs and genes retrieval from TropGene, Gramene and Ensembl

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Wsdl

Wsdl Operation

Xpath Expression

Wsdl

Wsdl Operation

Wsdl

Wsdl Operation

Xpath Expression

Xpath Expression

Script

Wsdl

Wsdl Operation

Xpath Expression

Wsdl

Wsdl Operation

Wsdl

Wsdl Operation

Xpath Expression

Xpath Expression

Wsdl

Wsdl Operation

Xpath Expression

Script

Script

Reviews (0)

Comments (0)

Other workflows that use similar services (0)