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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/hmm.ehmmcalibrate
WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/hmm.ehmmcalibrate?wsdl(download last cached WSDL file)
Documentation URL(s): SoapLab Support (over 10 years ago) http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/ehmmcalibrate.html Login to add a documentation URL Description(s): from provider’s description doc (over 10 years ago) Calibrate HMM search statistics
SoapLab Support(over 10 years ago)
Calibrate HMM search statistics
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 : ehmmcalibrate
- installation : Soaplab2 default installation
- type : HMM
- output :
- description : Calibrate HMM search statistics
- version : 6.1.0
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : ehmmcalibrate
- installation : Soaplab2 default installation
- type : HMM
- output :
- description : Calibrate HMM search statistics
- 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 : hmm
- help_url : http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/ehmmcalibrate.html
- parameter :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- data :
- result :
- iotype : output
- base :
- range :
- format : %d
- min : 0
- repeatable :
- base :
- name : cpu
- help : Sets the maximum number of CPUs that the program will run on. The default is to use all CPUs in the machine. Overrides the HMMER NCPU environment variable. Only affects threaded versions of HMMER (the default on most systems).
- default : 0
- mandatory : false
- qualifier : cpu
- prompt : Number of CPUs
- type : long
- ordering : 4
- range :
- format : %d
- min : 0
- repeatable :
- base :
- name : fixed
- help : Fix the length of the random sequences to , where is a positive (and reasonably sized) integer. The default is instead to generate sequences with a variety of different lengths, controlled by a Gaussian (normal) distribution.
- default : 0
- mandatory : false
- qualifier : fixed
- prompt : Length fix for random sequences
- type : long
- ordering : 5
- range :
- format : %f
- repeatable :
- base :
- name : mean
- help : Set the mean length of the synthetic sequences to , where is a positive real number. The default is 350.
- default : 350.0
- mandatory : false
- qualifier : mean
- prompt : Mean length of synthetic sequences
- type : float
- ordering : 6
- range :
- format : %d
- min : 0
- repeatable :
- base :
- name : num
- help : Set the number of synthetic sequences to , where is a positive integer. If is less than about 1000, the ft to the EVD may fail. Higher numbers of will give better determined EVD parameters. The default is 5000; it was empirically chosen as a tradeoff between accuracy and computation time.
- default : 5000
- mandatory : false
- qualifier : num
- prompt : Number of synthetic sequences
- type : long
- ordering : 7
- base :
- name : pvm
- help : Run on a Parallel Virtual Machine (PVM). The PVM must already be running. The client program hmmcalibrate-pvm must be installed on all the PVM nodes. Optional PVM support must have been compiled into HMMER.
- default : false
- mandatory : false
- qualifier : pvm
- prompt : Run on parallel virtual machines
- type : boolean
- ordering : 8
- range :
- format : %f
- min : 0
- repeatable :
- base :
- name : sd
- help : Set the standard deviation of the synthetic sequence length distribution to , where is a positive real number. The default is 350. Note that the Gaussian is left-truncated so that no sequences have lengths <= 0.
- default : 350.0
- mandatory : false
- qualifier : sd
- prompt : Standard deviation of syntheic sequences
- type : float
- ordering : 9
- range :
- format : %d
- min : 0
- repeatable :
- base :
- name : seed
- help : Set the random seed to , where is a positive integer. The default is to use time() to generate a different seed for each run, which means that two different runs of hmmcalibrate on the same HMM will give slightly different results. You can use this option to generate reproducible results for different hmmcalibrate runs on the same HMM.
- default : 0
- mandatory : false
- qualifier : seed
- prompt : Random seed
- type : long
- ordering : 10
- data :
- result :
- iotype : output
- base :
- data :
- option :
- input :
- name : cpu
- default : 0
- mandatory : false
- type : long
- name : fixed
- default : 0
- mandatory : false
- type : long
- name : mean
- default : 350.0
- mandatory : false
- type : float
- name : num
- default : 5000
- mandatory : false
- type : long
- name : pvm
- default : false
- mandatory : false
- type : boolean
- name : sd
- default : 350.0
- mandatory : false
- type : float
- name : seed
- default : 0
- mandatory : false
- type : long
- analysis :
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