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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:
Mike Mayer (over 9 years ago)
Base URL:
http://www.ebi.ac.uk/soaplab/services/alignment_multiple.showalign
WSDL Location:
http://www.ebi.ac.uk/soaplab/services/alignment_multiple.showalign?wsdl(download last cached WSDL file)
Documentation URL(s): None Login to add a documentation URL Description(s): No description(s) yet 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 8 years ago)
- ds_lsr_analysis :
- analysis :
- name : showalign
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Alignment Multiple, Display
- description : Display a multiple sequence alignment in pretty format
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : showalign
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Alignment Multiple, Display
- description : Display a multiple sequence alignment in pretty format
- analysis_extension :
- parameter :
- data :
- list :
- list_item :
- level : 0
- value : abi
- level : 0
- value : ace
- level : 0
- value : acedb
- level : 0
- value : bam
- level : 0
- value : biomart
- level : 0
- value : clustal
- level : 0
- value : codata
- level : 0
- value : dbid
- level : 0
- value : embl
- level : 0
- value : ensembl
- level : 0
- value : experiment
- level : 0
- value : fasta
- level : 0
- value : fastq
- level : 0
- value : fastq-illumina
- level : 0
- value : fastq-sanger
- level : 0
- value : fastq-solexa
- level : 0
- value : fitch
- level : 0
- value : gcg
- level : 0
- value : genbank
- level : 0
- value : genpept
- level : 0
- value : gff2
- level : 0
- value : gff3
- level : 0
- value : gifasta
- level : 0
- value : hennig86
- level : 0
- value : ig
- level : 0
- value : igstrict
- level : 0
- value : jackknifer
- level : 0
- value : mase
- level : 0
- value : mega
- level : 0
- value : msf
- level : 0
- value : nbrf
- level : 0
- value : nexus
- level : 0
- value : pdb
- level : 0
- value : pdbnuc
- level : 0
- value : pdbnucseq
- level : 0
- value : pdbseq
- level : 0
- value : pearson
- level : 0
- value : phylip
- level : 0
- value : phylipnon
- level : 0
- value : raw
- level : 0
- value : refseqp
- level : 0
- value : sam
- level : 0
- value : selex
- level : 0
- value : staden
- level : 0
- value : stockholm
- level : 0
- value : strider
- level : 0
- value : swiss
- level : 0
- value : text
- level : 0
- value : treecon
- type : full
- list_item :
- list :
- base :
- data :
- result :
- iotype : output
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- standard :
- repeatable :
- base :
- base :
- name : bottom
- ordering : 7
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : If this is true then the reference sequence is displayed at the bottom of the alignment instead of the top.
- default : false
- qualifier : bottom
- mandatory : false
- prompt : Display the reference sequence at the bottom
- type : boolean
- standard :
- list :
- list_item :
- shown_as : All of the sequences
- level : 0
- value : A
- shown_as : Identities between the sequences
- level : 0
- value : I
- shown_as : Non-identities between the sequences
- level : 0
- value : N
- shown_as : Similarities between the sequences
- level : 0
- value : S
- shown_as : Dissimilarities between the sequences
- level : 0
- value : D
- name : What to show
- type : full
- list_item :
- repeatable :
- list :
- base :
- standard :
- list :
- list_item :
- shown_as : Input order – no change
- level : 0
- value : I
- shown_as : Alphabetical order of the names
- level : 0
- value : A
- shown_as : Similarity to the reference sequence
- level : 0
- value : S
- name : Output order of the sequences
- type : full
- list_item :
- repeatable :
- list :
- base :
- base :
- name : similarcase
- ordering : 10
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- 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
- qualifier : similarcase
- mandatory : false
- prompt : Show similar residues in lower-case
- type : boolean
- base :
- name : consensus
- ordering : 11
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : If this is true then the consensus line is displayed.
- default : false
- qualifier : consensus
- mandatory : false
- prompt : Display the consensus line
- type : boolean
- standard :
- repeatable :
- base :
- base :
- name : number
- ordering : 15
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- 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
- qualifier : number
- mandatory : false
- prompt : Number the sequences
- type : boolean
- base :
- name : ruler
- ordering : 16
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : If this option is true then a ruler line marking every 5th and 10th character in the alignment is displayed.
- default : false
- qualifier : ruler
- mandatory : false
- prompt : Display ruler
- type : boolean
- range :
- format : %d
- min : 1
- repeatable :
- base :
- name : width
- ordering : 17
- option :
- name : EDAM:0002136
- type : normal
- value : data Sequence width
- name : scalemin
- type : style
- value : 1
- default : 60
- qualifier : width
- mandatory : false
- prompt : Width of sequence to display
- type : long
- range :
- format : %d
- min : -1
- repeatable :
- base :
- name : margin
- ordering : 18
- option :
- name : EDAM:0002152
- type : normal
- value : data Rendering parameter
- name : scalemin
- type : style
- value : -1
- 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
- qualifier : margin
- mandatory : false
- prompt : Length of margin for sequence names
- type : long
- base :
- name : html
- ordering : 19
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- default : false
- qualifier : html
- mandatory : false
- prompt : Use HTML formatting
- type : boolean
- standard :
- repeatable :
- base :
- range :
- format : %f
- max : 100.0
- min : 0.0
- repeatable :
- base :
- name : plurality
- ordering : 21
- option :
- name : EDAM:0002146
- type : normal
- value : data Threshold
- name : scalemax
- type : style
- value : 100.0
- name : scalemin
- type : style
- value : 0.0
- 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
- qualifier : plurality
- mandatory : false
- prompt : Plurality check % for consensus
- type : float
- range :
- format : %f
- repeatable :
- base :
- name : setcase
- ordering : 22
- option :
- name : EDAM:0002146
- type : normal
- value : data Threshold
- name : calculated_default
- type : normal
- value : ${sequence.totweight} / 2
- 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.
- qualifier : setcase
- mandatory : false
- prompt : Threshold above which the consensus is given in uppercase
- type : float
- range :
- format : %f
- max : 100.0
- min : 0.0
- repeatable :
- base :
- name : identity
- ordering : 23
- option :
- name : EDAM:0002146
- type : normal
- value : data Threshold
- name : scalemax
- type : style
- value : 100.0
- name : scalemin
- type : style
- value : 0.0
- 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
- qualifier : identity
- mandatory : false
- prompt : Required % of identities at a position for consensus
- type : float
- base :
- name : gaps
- ordering : 24
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- 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
- qualifier : gaps
- mandatory : false
- prompt : Use gap characters in consensus
- type : boolean
- data :
- option :
- name : EDAM:0000091
- type : normal
- value : topic Database and file management
- name : EDAM:0000182
- type : normal
- value : topic Sequence alignment
- name : EDAM:0000562
- type : normal
- value : operation Sequence alignment reformatting
- name : emboss
- type : normal
- value : true
- name : installation
- type : normal
- value : Soaplab2 default installation
- name : version
- type : normal
- value : 6.3.0
- app_info :
- category : alignment_multiple
- help_url : http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/showalign.html
- event :
- action :
- id : _E_1
- parameter :
- 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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