EMBOSS cons SOAP Soaplab

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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:

Provider:
European Bioinformatics Institute (EBI)

Location:
United Kingdom

Submitter / Source:
uludag (about 1 year ago)

Base URL:
http://www.ebi.ac.uk:80/soaplab/typed/services/alignment_consensus.cons

WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/alignment_consensus.cons?wsdl(download last cached WSDL file)

Soaplab Server Base URL:
http://www.ebi.ac.uk:80/soaplab/typed/services

Soaplab Server WSDL:
http://www.ebi.ac.uk/soaplab/typed/services/list?wsdl

Documentation URL(s): uludag (about 1 year ago)http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/cons.html

Login to add a documentation URL Description(s): from provider’s description doc (6 months ago) Create a consensus sequence from a multiple alignment

uludag (about 1 year ago)Create a consensus sequence from a multiple alignment

Login to add a description Details (from Soaplab server): from Soaplab server(6 months ago)

  • ds_lsr_analysis :
    • analysis :
      • name : cons
      • type : Alignment Consensus
      • installation : Soaplab2 default installation
      • output :
      • version : 6.1.0
      • description : Create a consensus sequence from a multiple alignment
      • input :
      • analysis_extension :

Show all

  • ds_lsr_analysis :
    • analysis :
      • name : cons
      • type : Alignment Consensus
      • installation : Soaplab2 default installation
      • output :
      • version : 6.1.0
      • description : Create a consensus sequence from a multiple alignment
      • input :
        • name : identity
        • default : 0
        • mandatory : false
        • type : long
      • 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_consensus
          • help_url : http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/cons.html
        • parameter :
          • base :
          • 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
          • base :
          • data :
            • ioformat : unspecified
            • iotype : input
            • repeatable :
          • range :
            • format : %f
            • repeatable :
          • base :
            • name : plurality
            • help : Set a cut-off for the number of positive matches below which there is no consensus. The default plurality is taken as half the total weight of all the sequences in the alignment.
            • qualifier : plurality
            • mandatory : false
            • option :
              • name : calculated_default
              • type : normal
              • value : ${sequence.totweight} / 2
            • type : float
            • prompt : Plurality check value
            • ordering : 6
          • range :
            • format : %d
            • min : 0
            • repeatable :
          • base :
            • name : identity
            • default : 0
            • help : Provides the facility of setting the required number of identities at a site for it to give a consensus at that position. Therefore, if this is set to the number of sequences in the alignment only columns of identities contribute to the consensus.
            • qualifier : identity
            • mandatory : false
            • type : long
            • prompt : Required number of identities at a position
            • ordering : 7
          • range :
            • format : %f
            • repeatable :
          • base :
            • name : setcase
            • help : Sets the threshold for the positive matches above which the consensus is is upper-case and below which the consensus is in lower-case.
            • qualifier : setcase
            • mandatory : false
            • option :
              • name : calculated_default
              • type : normal
              • value : ${sequence.totweight} / 2
            • type : float
            • prompt : Define a threshold above which the consensus is given in uppercase
            • ordering : 8
          • base :
          • data :
            • result :
            • iotype : output
          • standard :
            • repeatable :
          • base :
          • standard :
            • 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
            • repeatable :
          • base :

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