The Tool ID for this interface is PARALLELSTRUCTURE_XSEDE.
It is selected with toolId=PARALLELSTRUCTURE_XSEDE
The interface was updated on 6/30/2021 as part of moving the code form the machine Comet to the machine Expanse.
There is one change in the interface that is required, the new paramter is shown in red below.
Supported uploaded files:
input.infile_ = Primary Input File
input.joblist_file_ = this is the job list. will be named joblist.txt required
Supported parameters are:
vparam.runtime_ = (Float) Maximum Hours to Run. Max = 168, default=0.5.
vparam.specify_threads_ = (Integer) How many jobs are in your job list file? No default. (new; required)
vparam.set_numinds_ = (Integer, no default) Number of individuals in the population. Required.
vparam.set_numloci_ = (Integer, no default) Number of loci in the dataset. Required.
vparam.set_ploidy_ = (Integer, no default) Ploidy of the dataset. Required value
vparam.set_missing_ = (Integer, no default) Value given to missing genotype data. Required.
vparam.set_onerowperind_ = (Switch, default=0) The data for each individual are arranged in a single row.
vparam.set_labels_ = (Switch, default=0) Input file contains labels (names) for each individual.
vparam.use_popinfo_ = (Switch, default=0) Use prior population information to assign individuals to clusters
vparam.revert_convert_ = (Switch, default=0) Convert population IDs back into the original data file IDs. Only when usepopinfo_=1
vparam.set_popdata_ = (Switch, default=0) Input file contains a user-defined population-of-origin for each individual.
vparam.set_popflag_ = (Switch, default=0) Input file contains an indicator variable which says whether to use popinfo only when use_popinfo=1.
vparam.set_locdata_ = (Switch, default=0) Input file contains a user-defined sampling location for each individual only when use_locprior=1
vparam.set_phenotype_ = (Switch, default=0) Input file contains a column of phenotype information.
vparam.set_extracols_ = (Integer, no default) Number of additional columns of data after the Phenotype before the genotype data start.
vparam.set_markernames_ = (Switch, default=0) The top row of the data file contains a list of L names corresponding to the markers used.
vparam.set_recessivealleles_ = (Switch, default=0) Next row of data file contains a list of L integers indicating which alleles are recessive at each locus.
vparam.set_mapdistances_ = (Switch, default=0) The next row of the data file contains a list of mapdistances between neighboring loci (MAPDISTANCES)
vparam.use_linkagemodel_ = (Switch, default=0) Use the linkage model.
vparam.set_phased_ = (Switch, default=0) Indicates that data are in correct phase, use_linkagemodel=1
vparam.set_phaseinfo_ = (Switch, default=0) The row(s) of genotype data for each individual are followed by a row of information about haplotype phase, only when use_linkagemodel=1 & set_phased = 0
vparam.set_noadmix_ = (Switch, default=0) Assume the model without admixture
vparam.use_locprior_ = (Switch, default=0) Use location information to improve the performance on data that are weakly informative about structure
vparam.use_inferalpha_ = (Switch, default=0) Infer the value of the model parameter alpha from the data, only when set_noadmix=0
vparam.use_popalphas_ = (Switch, default=0) Infer a separate alpha for each population.
vparam.set_alpha_ = (float, no default) Dirichlet parameter for degree of admixture.
vparam.use_unifprioralpha_ = (Switch) Assume a uniform prior for alpha which runs between 0 and ALPHAMAX
vparam.specify_alphamax_ = (Float) Set the value for Alpha Max (ALPHAMAX)
vparam.use_inferlambda_ = (Switch, dfault=0) Infer a suitable value for lambda (INFERLAMBDA)
vparam.use_freqscorr_ = (Float, no default) Use the F model, in which the allele frequencies are correlated across populations.
vparam.set_fpriormean_ = (Float, no default) Set mean FPRIORMEAN for Fk.
vparam.set_fpriorsd_ = (Float, no default) Set std deviation for Fk.
vparam.use_onefst_= (Switch, default=0) Assume the same value of Fk for all populations.
vparam.set_gensback_= (integer, no default) Set value for G. Only when use_popinfo=1
vparam.set_migrprior_ = (Float, no default) Set migration prior. Sensible values might be in the range 0.001—0.1.
vparam.use_pfrompopflagonly_ = (Switch, default=0) Update the allele frequencies, P , using only a prespecified subset of the individuals, only when set_popflag=1
vparam.use_locispop_ = (Switch, default=0) Use the PopData Column for Location data.
vparam.set_locpriorinit_= (float, default=1) Initial value for the LOCPRIOR parameter r.
vparam.set_maxlocprior_= (Integer, default=20) MAXLOCPRIOR (double) Range of r is from (0,MAXLOCPRIOR).
Miscellaneous options
vparam.specify_alphapropsd_ = (Float, no default) Set the value for alphapropsd (ALPHAPROPSD)
vparam.print_loglikeli_ = (Switch, default=0) Print the log-likelihood of the data at each update (COMPUTEPROB)
vparam.use_metrofreq_ = (Integer, no default) Frequency of using a Metropolis-Hastings step (METROFREQ)
Output options
vparam.set_printnet_ = (Switch) Print the net nucleotide distance between clusters (PRINTNET)
vparam.set_printqhat_= (Switch) default=0 When this is turned on, the point estimate for Q is not only printed into the main results file, but also into a separate file with suffix “q”. This file is required in order to run the companion program STRAT.
vparam.set_ancestdist_ = (Switch) default=0 Collect information about the distribution of Q for each individual (ANCESTDIST)
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