This looks like a Soaplab service. Click here for more info and guidance on how to use this service )
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/nucleic_gene_finding.tcode
WSDL Location:
http://www.ebi.ac.uk/soaplab/services/nucleic_gene_finding.tcode?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 : tcode
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Nucleic Gene finding
- description : Identify protein-coding regions using Fickett TESTCODE statistic
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : tcode
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Nucleic Gene finding
- description : Identify protein-coding regions using Fickett TESTCODE statistic
- 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 :
- range :
- format : %d
- max :
- min : 1
- repeatable :
- base :
- name : step
- ordering : 9
- option :
- name : EDAM:0002141
- type : normal
- value : data Window step size
- name : calculated_hardmax
- type : normal
- value : ${sequence.length} – ${window}
- name : scalemin
- type : style
- value : 1
- help : The selected window will, by default, slide along the nucleotide sequence by three bases at a time, retaining the frame (although the algorithm is not frame sensitive). This may be altered to increase or decrease the increment of the slide.
- default : 3
- qualifier : step
- mandatory : false
- prompt : Stepping increment for the window
- type : long
- standard :
- list :
- list_item :
- shown_as : Portable Network Graphics (png)
- level : 0
- value : png
- shown_as : Postscript
- level : 0
- value : colourps
- type : full
- list_item :
- repeatable :
- list :
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- range :
- format : %d
- max :
- min : 200
- repeatable :
- base :
- name : window
- ordering : 6
- option :
- name : EDAM:0001251
- type : normal
- value : data Window size
- name : calculated_hardmax
- type : normal
- value : ${sequence.length}
- name : scalemin
- type : style
- value : 200
- help : This is the number of nucleotide bases over which the TESTCODE statistic will be performed each time. The window will then slide along the sequence, covering the same number of bases each time.
- default : 200
- qualifier : window
- mandatory : false
- prompt : Length of sliding window
- type : long
- base :
- name : plot
- ordering : 11
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : On selection a graph of the sequence (X axis) plotted against the coding score (Y axis) will be displayed. Sequence above the green line is coding, that below the red line is non-coding.
- default : false
- qualifier : plot
- mandatory : false
- prompt : Graphical display
- type : boolean
- data :
- result :
- iotype : output
- base :
- data :
- result :
- iotype : output
- base :
- data :
- result :
- iotype : output
- base :
- name : Graphics_in_PNG
- ordering : 13
- option :
- name : EDAM:0002160
- type : normal
- value : data Fickett testcode plot
- name : allow_non_existent
- type : normal
- value : true
- name : datatype
- type : normal
- value : bindata
- name : mimetype
- type : normal
- value : image/png
- name : nodisplay
- type : style
- value : true
- method : %%%Graphics_in_PNG%%% ${Graphics_in_PNG}
- qualifier : Graphics_in_PNG
- mandatory : false
- type : byte[][]
- data :
- option :
- name : EDAM:0000109
- type : normal
- value : topic Gene finding
- name : EDAM:0000436
- type : normal
- value : operation Coding region prediction
- 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 : nucleic_gene_finding
- help_url : http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/tcode.html
- event :
- action :
- id : _E_1
- parameter :
- input :
- name : step
- default : 3
- mandatory : false
- type : long
- name : window
- default : 200
- mandatory : false
- type : long
- name : plot
- default : false
- mandatory : false
- type : boolean
- analysis :
License(s): No info yet Login to add license info Cost: No info yet Login to add cost info Usage conditions: No info yet Login to add usage conditions info Contact info: No info yet Login to add contact info How to cite this service: No info yet Login to add how to cite info Publications about this service: for this service (this can be in a common citation format like Bibtex, MLA or APA, a DOI, a URL, etc.) No info yet Login to add publications info Citations of this service: No info yet Login to add citations info Example workflows using this service: See all workflows on myExperiment that use this service Login to add workflows info