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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 (almost 12 years ago)
Base URL:
http://www.ebi.ac.uk:80/soaplab/typed/services/display.showalign
WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/display.showalign?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 a multiple sequence alignment 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 : showalign
- installation : Soaplab2 default installation
- type : Alignment Multiple, Display
- output :
- description : Display a multiple sequence alignment in pretty format
- version : 6.1.0
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : showalign
- installation : Soaplab2 default installation
- type : Alignment Multiple, Display
- output :
- description : Display a multiple sequence alignment 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 : alignment_multiple
- help_url : http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/showalign.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 :
- iotype : output
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- standard :
- repeatable :
- base :
- base :
- name : bottom
- help : If this is true then the reference sequence is displayed at the bottom of the alignment as well as at the top.
- default : false
- mandatory : false
- qualifier : bottom
- prompt : Display the reference sequence at the bottom
- type : boolean
- ordering : 7
- standard :
- list :
- name : What to show
- list_item :
- level : 0
- shown_as : All of the sequences
- value : A
- level : 0
- shown_as : Identities between the sequences
- value : I
- level : 0
- shown_as : Non-identities between the sequences
- value : N
- level : 0
- shown_as : Similarities between the sequences
- value : S
- level : 0
- shown_as : Dissimilarities between the sequences
- value : D
- type : full
- repeatable :
- list :
- base :
- standard :
- list :
- name : Output order of the sequences
- list_item :
- level : 0
- shown_as : Input order – no change
- value : I
- level : 0
- shown_as : Alphabetical order of the names
- value : A
- level : 0
- shown_as : Similarity to the reference sequence
- value : S
- type : full
- repeatable :
- list :
- base :
- base :
- name : similarcase
- help : If this is set True, then when -show is set to ‘Similarities’ or ‘Non-identities’ and a residue is similar but not identical to the reference sequence residue, it will be changed to lower-case. If -show is set to ‘All’ then non-identical, non-similar residues will be changed to lower-case. If this is False then no change to the case of the residues is made on the basis of their similarity to the reference sequence.
- default : false
- mandatory : false
- qualifier : similarcase
- prompt : Show similar residues in lower-case
- type : boolean
- ordering : 10
- base :
- name : consensus
- help : If this is true then the consensus line is displayed.
- default : false
- mandatory : false
- qualifier : consensus
- prompt : Display the consensus line
- type : boolean
- ordering : 11
- standard :
- repeatable :
- base :
- base :
- name : number
- help : If this option is true then a line giving the positions in the alignment is displayed every 10 characters above the alignment.
- default : false
- mandatory : false
- qualifier : number
- prompt : Number the sequences
- type : boolean
- ordering : 15
- base :
- name : ruler
- help : If this option is true then a ruler line marking every 5th and 10th character in the alignment is displayed.
- default : false
- mandatory : false
- qualifier : ruler
- prompt : Display ruler
- type : boolean
- ordering : 16
- range :
- format : %d
- min : 1
- repeatable :
- base :
- name : width
- default : 60
- option :
- name : scalemin
- type : style
- value : 1
- mandatory : false
- qualifier : width
- prompt : Width of sequence to display
- type : long
- ordering : 17
- range :
- format : %d
- min : -1
- repeatable :
- base :
- name : margin
- help : This sets the length of the left-hand margin for sequence names. If the margin is set at 0 then no margin and no names are displayed. If the margin is set to a value that is less than the length of a sequence name then the sequence name is displayed truncated to the length of the margin. If the margin is set to -1 then the minimum margin width that will allow all the sequence names to be displayed in full plus a space at the end of the name will automatically be selected.
- default : -1
- option :
- name : scalemin
- type : style
- value : -1
- mandatory : false
- qualifier : margin
- prompt : Length of margin for sequence names
- type : long
- ordering : 18
- base :
- name : html
- default : false
- mandatory : false
- qualifier : html
- prompt : Use HTML formatting
- type : boolean
- ordering : 19
- standard :
- repeatable :
- base :
- range :
- format : %f
- max : 100.0
- min : 0.0
- repeatable :
- base :
- name : plurality
- help : Set a cut-off for the % of positive scoring matches below which there is no consensus. The default plurality is taken as 50% of the total weight of all the sequences in the alignment.
- default : 50.0
- option :
- name : scalemax
- type : style
- value : 100.0
- name : scalemin
- type : style
- value : 0.0
- mandatory : false
- qualifier : plurality
- prompt : Plurality check % for consensus
- type : float
- ordering : 21
- range :
- format : %f
- repeatable :
- base :
- name : setcase
- help : Sets the threshold for the scores of the positive matches above which the consensus is in upper-case and below which the consensus is in lower-case. By default this is set to be half of the (weight-adjusted) number of sequences in the alignment.
- option :
- name : calculated_default
- type : normal
- value : ${sequence.totweight} / 2
- mandatory : false
- qualifier : setcase
- prompt : Threshold above which the consensus is given in uppercase
- type : float
- ordering : 22
- range :
- format : %f
- max : 100.0
- min : 0.0
- repeatable :
- base :
- name : identity
- help : Provides the facility of setting the required number of identities at a position for it to give a consensus. Therefore, if this is set to 100% only columns of identities contribute to the consensus.
- default : 0.0
- option :
- name : scalemax
- type : style
- value : 100.0
- name : scalemin
- type : style
- value : 0.0
- mandatory : false
- qualifier : identity
- prompt : Required % of identities at a position for consensus
- type : float
- ordering : 23
- base :
- name : gaps
- help : If this option is true then gap characters can appear in the consensus. The alternative is ‘N’ for nucleotide, or ‘X’ for protein
- default : false
- mandatory : false
- qualifier : gaps
- prompt : Use gap characters in consensus
- type : boolean
- ordering : 24
- data :
- option :
- input :
- name : bottom
- default : false
- mandatory : false
- type : boolean
- name : similarcase
- default : false
- mandatory : false
- type : boolean
- name : consensus
- default : false
- mandatory : false
- type : boolean
- name : number
- default : false
- mandatory : false
- type : boolean
- name : ruler
- default : false
- mandatory : false
- type : boolean
- name : width
- default : 60
- mandatory : false
- type : long
- name : margin
- default : -1
- mandatory : false
- type : long
- name : html
- default : false
- mandatory : false
- type : boolean
- name : plurality
- default : 50.0
- mandatory : false
- type : float
- name : identity
- default : 0.0
- mandatory : false
- type : float
- name : gaps
- default : false
- mandatory : false
- type : boolean
- analysis :
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