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About Soaplab
Soaplab services are command line applications, wrapped as SOAP services, and served from a Soaplab server. All Soaplab services have the same generic set of SOAP operations (depending on the Soaplab version) as they all share a standardised interface.
Certain tools, like the Taverna workflow workbench, provide automatic support for the Soaplab way of executing these services. In some cases you will need to use the Soaplab Server Base URL rather than the WSDL location in these tools.
More information on Soaplab clients is available here.
Further documentation on Soaplab services is available:
- Soaplab overview
- Soaplab client guide page
- EBI Soaplab server documentation
- Soaplab 2
- Sourceforge site for EMBOSS Soaplab services
Provider:
European Bioinformatics Institute (EMBL-EBI)
Location:
United Kingdom
Submitter/Source:
SoapLab Support (over 11 years ago)
Base URL:
http://www.ebi.ac.uk:80/soaplab/typed/services/feature_tables.showfeat
WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/feature_tables.showfeat?wsdl(download last cached WSDL file)
Documentation URL(s): None Login to add a documentation URL Description(s): from provider’s description doc (over 10 years ago) Display features of a sequence in pretty format
Login to add a description ELIXIR Description(s): No info yet Login to add an elixir description Details (from Soaplab server): from Soaplab server(over 10 years ago)
- ds_lsr_analysis :
- analysis :
- name : showfeat
- installation : Soaplab2 default installation
- type : Display, Feature tables
- output :
- description : Display features of a sequence in pretty format
- version : 6.1.0
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : showfeat
- installation : Soaplab2 default installation
- type : Display, Feature tables
- output :
- description : Display features of a sequence in pretty format
- version : 6.1.0
- analysis_extension :
- option :
- name : emboss
- type : normal
- value : true
- name : installation
- type : normal
- value : Soaplab2 default installation
- name : version
- type : normal
- value : 6.1.0
- event :
- action :
- id : _E_1
- app_info :
- category : display
- help_url : http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/showfeat.html
- parameter :
- data :
- list :
- list_item :
- level : 0
- value : gcg
- level : 0
- value : gcg8
- level : 0
- value : embl
- level : 0
- value : swiss
- level : 0
- value : fasta
- level : 0
- value : ncbi
- level : 0
- value : genbank
- level : 0
- value : nbrf
- level : 0
- value : pir
- level : 0
- value : codata
- level : 0
- value : strider
- level : 0
- value : clustal
- level : 0
- value : phylip
- level : 0
- value : acedb
- level : 0
- value : msf
- level : 0
- value : jackknifer
- level : 0
- value : jackknifernon
- level : 0
- value : nexus
- level : 0
- value : nexusnon
- level : 0
- value : treecon
- level : 0
- value : mega
- level : 0
- value : meganon
- level : 0
- value : ig
- level : 0
- value : staden
- level : 0
- value : text
- level : 0
- value : raw
- type : full
- list_item :
- list :
- base :
- data :
- result :
- extension : showfeat
- iotype : output
- base :
- standard :
- repeatable :
- base :
- standard :
- repeatable :
- base :
- standard :
- repeatable :
- base :
- standard :
- repeatable :
- base :
- standard :
- list :
- name : Sorting features
- list_item :
- level : 0
- shown_as : Sort by Source
- value : source
- level : 0
- shown_as : Sort by Start position
- value : start
- level : 0
- shown_as : Sort by Type
- value : type
- level : 0
- shown_as : No sorting done
- value : nosort
- type : full
- repeatable :
- list :
- base :
- base :
- name : joinfeatures
- default : false
- mandatory : false
- qualifier : joinfeatures
- prompt : Join coding regions together
- type : boolean
- ordering : 9
- standard :
- repeatable :
- base :
- base :
- name : html
- default : false
- mandatory : false
- qualifier : html
- prompt : Use HTML formatting
- type : boolean
- ordering : 13
- base :
- name : id
- help : Set this to be false if you do not wish to display the ID name of the sequence.
- default : false
- mandatory : false
- qualifier : id
- prompt : Show sequence ID
- type : boolean
- ordering : 14
- base :
- name : description
- help : Set this to be false if you do not wish to display the description of the sequence.
- default : false
- mandatory : false
- qualifier : description
- prompt : Show description
- type : boolean
- ordering : 15
- base :
- name : scale
- help : Set this to be false if you do not wish to display the scale line.
- default : false
- mandatory : false
- qualifier : scale
- prompt : Show scale line
- type : boolean
- ordering : 16
- range :
- format : %d
- min : 0
- repeatable :
- base :
- name : width
- help : You can expand (or contract) the width of the ASCII-character graphics display of the positions of the features using this value. For example, a width of 80 characters would cover a standard page width and a width a 10 characters would be nearly unreadable. If the width is set to less than 4, the graphics lines and the scale line will not be displayed.
- default : 60
- mandatory : false
- qualifier : width
- prompt : Width of graphics lines
- type : long
- ordering : 17
- base :
- name : collapse
- help : If this is set, then features from the same source and of the same type and sense are all printed on the same line. For instance if there are several features from the EMBL feature table (ie. the same source) which are all of type ‘exon’ in the same sense, then they will all be displayed on the same line. This makes it hard to distinguish overlapping features. If this is set to false then each feature is displayed on a separate line making it easier to distinguish where features start and end.
- default : false
- mandatory : false
- qualifier : collapse
- prompt : Display features with the same type on one line
- type : boolean
- ordering : 18
- base :
- name : forward
- help : Set this to be false if you do not wish to display forward sense features.
- default : false
- mandatory : false
- qualifier : forward
- prompt : Display forward sense features
- type : boolean
- ordering : 19
- base :
- name : reverse
- help : Set this to be false if you do not wish to display reverse sense features.
- default : false
- mandatory : false
- qualifier : reverse
- prompt : Display reverse sense features
- type : boolean
- ordering : 20
- base :
- name : unknown
- help : Set this to be false if you do not wish to display unknown sense features. (ie. features with no directionality – all protein features are of this type and some nucleic features (for example, CG-rich regions)).
- default : false
- mandatory : false
- qualifier : unknown
- prompt : Display unknown sense features
- type : boolean
- ordering : 21
- base :
- name : strand
- help : Set this if you wish to display the strand of the features. Protein features are always directionless (indicated by ‘0’), forward is indicated by ‘+’ and reverse is ‘-‘.
- default : false
- mandatory : false
- qualifier : strand
- prompt : Display strand of features
- type : boolean
- ordering : 22
- base :
- name : origin
- help : Set this if you wish to display the origin of the features. The source name is usually either the name of the program that detected the feature or it is the name of the feature table (eg: EMBL) that the feature came from.
- default : false
- mandatory : false
- qualifier : origin
- prompt : Display source of features
- type : boolean
- ordering : 23
- base :
- name : position
- help : Set this if you wish to display the start and end position of the features. If several features are being displayed on the same line, then the start and end positions will be joined by a comma, for example: ‘189-189,225-225’.
- default : false
- mandatory : false
- qualifier : position
- prompt : Display position of features
- type : boolean
- ordering : 24
- base :
- name : type
- help : Set this to be false if you do not wish to display the type of the features.
- default : false
- mandatory : false
- qualifier : type
- prompt : Display type of features
- type : boolean
- ordering : 25
- base :
- name : tags
- help : Set this to be false if you do not wish to display the tags and values of the features.
- default : false
- mandatory : false
- qualifier : tags
- prompt : Display tags of features
- type : boolean
- ordering : 26
- base :
- name : values
- help : Set this to be false if you do not wish to display the tag values of the features. If this is set to be false, only the tag names will be displayed. If the tags are not displayed, then the values will not be displayed. The value of the ‘translation’ tag is never displayed as it is often extremely long.
- default : false
- mandatory : false
- qualifier : values
- prompt : Display tag values of features
- type : boolean
- ordering : 27
- base :
- name : stricttags
- help : By default if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed. If this is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed.
- default : false
- mandatory : false
- qualifier : stricttags
- prompt : Only display the matching tags
- type : boolean
- ordering : 28
- data :
- option :
- input :
- name : joinfeatures
- default : false
- mandatory : false
- type : boolean
- name : html
- default : false
- mandatory : false
- type : boolean
- name : id
- default : false
- mandatory : false
- type : boolean
- name : description
- default : false
- mandatory : false
- type : boolean
- name : scale
- default : false
- mandatory : false
- type : boolean
- name : width
- default : 60
- mandatory : false
- type : long
- name : collapse
- default : false
- mandatory : false
- type : boolean
- name : forward
- default : false
- mandatory : false
- type : boolean
- name : reverse
- default : false
- mandatory : false
- type : boolean
- name : unknown
- default : false
- mandatory : false
- type : boolean
- name : strand
- default : false
- mandatory : false
- type : boolean
- name : origin
- default : false
- mandatory : false
- type : boolean
- name : position
- default : false
- mandatory : false
- type : boolean
- name : type
- default : false
- mandatory : false
- type : boolean
- name : tags
- default : false
- mandatory : false
- type : boolean
- name : values
- default : false
- mandatory : false
- type : boolean
- name : stricttags
- default : false
- mandatory : false
- type : boolean
- analysis :
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