structure: structure.xml annotate

annotate structure.xml @ 0:a1574aada200 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb

author	iuc
date	Wed, 15 Nov 2017 16:31:24 -0500
parents
children	64e681a1cad5

rev	line source
0 a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	1 <tool id="structure" name="Structure" version="2.3.4">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	2 <description>using multi-locus genotype data to investigate population structure</description>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	3 <requirements>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	4 <requirement type="package" version="2.3.4">structure</requirement>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	5 </requirements>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	6 <version_command><![CDATA[
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	7 structure \| grep -E -o 'Version.+'
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	8 ]]></version_command>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	9 <command detect_errors="exit_code"><![CDATA[
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	10 mv '$mainparams' '$out_mainparams' &&
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	11 mv '$extraparams' '$out_extraparams' &&
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	12
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	13 mkdir out log
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	14
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	15 #for $run in range(1, int($nb_run) + 1):
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	16 && structure -i '$infile' -o outfile -m '$out_mainparams' -e '$out_extraparams' > 'log/run${run}_K_${main.MAXPOPS}.log'
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	17 && mv 'outfile_f' 'out/run${run}_K_${main.MAXPOPS}.out'
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	18 #end for
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	19
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	20 ]]></command>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	21 <configfiles>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	22 <configfile name="mainparams"><![CDATA[
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	23 KEY PARAMETERS FOR THE PROGRAM structure. YOU WILL NEED TO SET THESE
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	24 IN ORDER TO RUN THE PROGRAM. VARIOUS OPTIONS CAN BE ADJUSTED IN THE
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	25 FILE extraparams.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	26
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	27
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	28 "(int)" means that this takes an integer value.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	29 "(B)" means that this variable is Boolean
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	30 (ie insert 1 for True, and 0 for False)
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	31 "(str)" means that this is a string (but not enclosed in quotes!)
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	32
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	33
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	34 Basic Program Parameters
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	35
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	36 #define MAXPOPS $main.MAXPOPS // default:2 // (int) number of populations assumed
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	37 #define BURNIN $main.BURNIN // default:10000 // (int) length of burnin period
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	38 #define NUMREPS $main.NUMREPS // default:20000 // (int) number of MCMC reps after burnin
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	39
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	40 Input/Output files
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	41
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	42 #define INFILE $infile // (str) name of input data file
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	43 #define OUTFILE outfile //(str) name of output data file
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	44
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	45 Data file format
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	46
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	47 #define NUMINDS $main.NUMINDS // default:100 // (int) number of diploid individuals in data file
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	48 #define NUMLOCI $main.NUMLOCI // default:100 // (int) number of loci in data file
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	49 #define PLOIDY $main.PLOIDY // default:2 // (int) ploidy of data
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	50 #define MISSING $main.MISSING // default:-9 // (int) value given to missing genotype data
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	51 #define ONEROWPERIND $main.ONEROWPERIND // default:0 // (B) store data for individuals in a single line
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	52
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	53
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	54 #define LABEL $main.LABEL // default:1 // (B) Input file contains individual labels
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	55 #define POPDATA $main.POPDATA // default:1 // (B) Input file contains a population identifier
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	56 #define POPFLAG ${extra.usepopinfo_cond.POPFLAG} // default:0 // (B) Input file contains a flag which says
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	57 whether to use popinfo when USEPOPINFO==1
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	58 #define LOCDATA $main.LOCDATA // default:0 // (B) Input file contains a location identifier
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	59
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	60 #define PHENOTYPE $main.PHENOTYPE // default:0 // (B) Input file contains phenotype information
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	61 #define EXTRACOLS $main.EXTRACOLS // default:0 // (int) Number of additional columns of data
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	62 before the genotype data start.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	63
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	64 #define MARKERNAMES $main.MARKERNAMES // default:1 // (B) data file contains row of marker names
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	65 #define RECESSIVEALLELES $main.recessivealleles_cond.RECESSIVEALLELES // default:0 // (B) data file contains dominant markers (eg AFLPs)
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	66 // and a row to indicate which alleles are recessive
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	67 #define MAPDISTANCES $main.MAPDISTANCES // default:0 // (B) data file contains row of map distances
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	68 // between loci
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	69
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	70
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	71 Advanced data file options
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	72
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	73 #define PHASED $main.PHASED // default:0 // (B) Data are in correct phase (relevant for linkage model only)
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	74 #define PHASEINFO $main.PHASEINFO // default:0 // (B) the data for each individual contains a line
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	75 indicating phase (linkage model)
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	76 #define MARKOVPHASE $main.MARKOVPHASE // default:0 // (B) the phase info follows a Markov model.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	77 #define NOTAMBIGUOUS $main.recessivealleles_cond.NOTAMBIGUOUS // default:-999 // (int) for use in some analyses of polyploid data
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	78
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	79
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	80
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	81 Command line options:
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	82
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	83 -m mainparams
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	84 -e extraparams
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	85 -s stratparams
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	86 -K MAXPOPS
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	87 -L NUMLOCI
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	88 -N NUMINDS
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	89 -i input file
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	90 -o output file
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	91 -D SEED
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	92
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	93 ]]></configfile>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	94 <configfile name="extraparams"><![CDATA[
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	95 EXTRA PARAMS FOR THE PROGRAM structure. THESE PARAMETERS CONTROL HOW THE
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	96 PROGRAM RUNS. ATTRIBUTES OF THE DATAFILE AS WELL AS K AND RUNLENGTH ARE
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	97 SPECIFIED IN mainparams.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	98
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	99 "(int)" means that this takes an integer value.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	100 "(d)" means that this is a double (ie, a Real number such as 3.14).
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	101 "(B)" means that this variable is Boolean
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	102 (ie insert 1 for True, and 0 for False).
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	103
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	104 PROGRAM OPTIONS
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	105
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	106 #define NOADMIX $extra.NOADMIX // default:0 // (B) Use no admixture model (0=admixture model, 1=no-admix)
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	107 #define LINKAGE $extra.LINKAGE // default:0 // (B) Use the linkage model model
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	108 #define USEPOPINFO $extra.usepopinfo_cond.USEPOPINFO // default:0 // (B) Use prior population information to pre-assign individuals
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	109 to clusters
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	110 #define LOCPRIOR $extra.LOCPRIOR // default:0 //(B) Use location information to improve weak data
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	111
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	112 #define FREQSCORR $extra.FREQSCORR // default:1 // (B) allele frequencies are correlated among pops
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	113 #define ONEFST $extra.ONEFST // default:0 // (B) assume same value of Fst for all subpopulations.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	114
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	115 #define INFERALPHA $extra.inferalpha_cond.INFERALPHA // default:1 // (B) Infer ALPHA (the admixture parameter)
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	116 #define POPALPHAS $extra.POPALPHAS // default:0 // (B) Individual alpha for each population
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	117 #define ALPHA $extra.inferalpha_cond.ALPHA // default:1.0 // (d) Dirichlet parameter for degree of admixture
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	118 (this is the initial value if INFERALPHA==1).
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	119
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	120 #define INFERLAMBDA $extra.inferlambda_cond.INFERLAMBDA // default:0 // (B) Infer LAMBDA (the allele frequencies parameter)
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	121 #define POPSPECIFICLAMBDA $extra.inferlambda_cond.POPSPECIFICLAMBDA // default:0 //(B) infer a separate lambda for each pop
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	122 (only if INFERLAMBDA=1).
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	123 #define LAMBDA $extra.LAMBDA // default:1.0 // (d) Dirichlet parameter for allele frequencies
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	124
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	125
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	126
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	127
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	128 PRIORS
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	129
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	130 #define FPRIORMEAN $extra.FPRIORMEAN // default:0.01 // (d) Prior mean and SD of Fst for pops.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	131 #define FPRIORSD $extra.FPRIORSD // default:0.05 // (d) The prior is a Gamma distribution with these parameters
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	132
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	133 #define UNIFPRIORALPHA $extra.unifprioralpha_cond.UNIFPRIORALPHA // default:1 // (B) use a uniform prior for alpha;
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	134 otherwise gamma prior
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	135 #define ALPHAMAX $extra.ALPHAMAX // default:10.0 // (d) max value of alpha if uniform prior
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	136 #define ALPHAPRIORA $extra.unifprioralpha_cond.ALPHAPRIORA // default:1.0 // (only if UNIFPRIORALPHA==0): alpha has a gamma
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	137 prior with mean A*B, and
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	138 #define ALPHAPRIORB $extra.unifprioralpha_cond.ALPHAPRIORB // default:2.0 // variance A*B^2.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	139
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	140
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	141 #define LOG10RMIN $extra.LOG10RMIN // default:-4.0 //(d) Log10 of minimum allowed value of r under linkage model
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	142 #define LOG10RMAX $extra.LOG10RMAX // default:1.0 //(d) Log10 of maximum allowed value of r
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	143 #define LOG10RPROPSD $extra.LOG10RPROPSD // default:0.1 //(d) standard deviation of log r in update
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	144 #define LOG10RSTART $extra.LOG10RSTART // default:-2.0 //(d) initial value of log10 r
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	145
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	146
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	147 USING PRIOR POPULATION INFO (USEPOPINFO)
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	148
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	149 #define GENSBACK $extra.GENSBACK // default:2 //(int) For use when inferring whether an indiv-
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	150 idual is an immigrant, or has an immigrant an-
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	151 cestor in the past GENSBACK generations. eg, if
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	152 GENSBACK==2, it tests for immigrant ancestry
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	153 back to grandparents.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	154 #define MIGRPRIOR $extra.usepopinfo_cond.MIGRPRIOR // default:0.01 //(d) prior prob that an individual is a migrant
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	155 (used only when USEPOPINFO==1). This should
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	156 be small, eg 0.01 or 0.1.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	157 #define PFROMPOPFLAGONLY $extra.PFROMPOPFLAGONLY // default:0 // (B) only use individuals with POPFLAG=1 to update P.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	158 This is to enable use of a reference set of
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	159 individuals for clustering additional "test"
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	160 individuals.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	161
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	162 LOCPRIOR MODEL FOR USING LOCATION INFORMATION
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	163
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	164 #define LOCISPOP $extra.LOCISPOP // default:1 //(B) use POPDATA for location information
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	165 #define LOCPRIORINIT $extra.LOCPRIORINIT // default:1.0 //(d) initial value for r, the location prior
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	166 #define MAXLOCPRIOR $extra.MAXLOCPRIOR // default:20.0 //(d) max allowed value for r
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	167
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	168
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	169
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	170
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	171 OUTPUT OPTIONS
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	172
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	173 #define PRINTNET $extra.PRINTNET // default:1 // (B) Print the "net nucleotide distance" to screen during the run
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	174 #define PRINTLAMBDA $extra.PRINTLAMBDA // default:1 // (B) Print current value(s) of lambda to screen
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	175 #define PRINTQSUM $extra.PRINTQSUM // default:1 // (B) Print summary of current population membership to screen
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	176
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	177 #define SITEBYSITE $extra.SITEBYSITE // default:0 // (B) whether or not to print site by site results.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	178 (Linkage model only) This is a large file!
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	179 #define PRINTQHAT $extra.PRINTQHAT // default:0 // (B) Q-hat printed to a separate file. Turn this
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	180 on before using STRAT.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	181 #define UPDATEFREQ $extra.UPDATEFREQ // default:100 // (int) frequency of printing update on the screen.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	182 Set automatically if this is 0.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	183 #define PRINTLIKES $extra.PRINTLIKES // default:0 // (B) print current likelihood to screen every rep
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	184 #define INTERMEDSAVE $extra.INTERMEDSAVE // default:0 // (int) number of saves to file during run
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	185
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	186 #define ECHODATA $extra.ECHODATA // default:1 // (B) Print some of data file to screen to check
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	187 that the data entry is correct.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	188 (NEXT 3 ARE FOR COLLECTING DISTRIBUTION OF Q:)
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	189 #define ANCESTDIST $extra.ANCESTDIST // default:0 // (B) collect data about the distribution of an-
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	190 cestry coefficients (Q) for each individual
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	191 #define NUMBOXES $extra.NUMBOXES // default:1000 // (int) the distribution of Q values is stored as
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	192 a histogram with this number of boxes.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	193 #define ANCESTPINT $extra.ANCESTPINT // default:0.90 // (d) the size of the displayed probability
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	194 interval on Q (values between 0.0--1.0)
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	195
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	196
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	197
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	198 MISCELLANEOUS
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	199
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	200 #define COMPUTEPROB $extra.COMPUTEPROB // default:1 // (B) Estimate the probability of the Data under
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	201 the model. This is used when choosing the
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	202 best number of subpopulations.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	203 #define ADMBURNIN $extra.ADMBURNIN // default:500 // (int) [only relevant for linkage model]:
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	204 Initial period of burnin with admixture model (see Readme)
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	205 #define ALPHAPROPSD $extra.ALPHAPROPSD // default:0.025 // (d) SD of proposal for updating alpha
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	206 #define STARTATPOPINFO $extra.STARTATPOPINFO // default:0 // Use given populations as the initial condition
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	207 for population origins. (Need POPDATA==1). It
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	208 is assumed that the PopData in the input file
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	209 are between 1 and k where k<=MAXPOPS.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	210 #define RANDOMIZE $extra.randomize_cond.RANDOMIZE // default:1 // (B) use new random seed for each run
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	211 #define SEED $extra.randomize_cond.SEED // default:2245 // (int) seed value for random number generator
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	212 (must set RANDOMIZE=0)
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	213 #define METROFREQ $extra.METROFREQ // default:10 // (int) Frequency of using Metropolis step to update
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	214 Q under admixture model (ie use the metr. move every
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	215 i steps). If this is set to 0, it is never used.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	216 (Proposal for each q^(i) sampled from prior. The
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	217 goal is to improve mixing for small alpha.)
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	218 #define REPORTHITRATE $extra.REPORTHITRATE // default:0 // (B) report hit rate if using METROFREQ
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	219
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	220 ]]></configfile>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	221 </configfiles>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	222 <inputs>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	223 <param name="infile" type="data" label="Genotype data" format="tabular" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	224 <param name="nb_run" value="1" type="integer" label="Number of runs" min="1" max="10" help="Note that the runs are sequential. Please launch separate runs if it's too long" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	225 <section name="main" title="mainparams" expanded="True">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	226 <!--Basic Program Parameters-->
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	227 <param argument="MAXPOPS" value="" type="integer" label="Number of populations assumed" help="or [K]"/>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	228 <param argument="BURNIN" value="10000" type="integer" label="Length of burnin period" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	229 <param argument="NUMREPS" value="20000" type="integer" label="Number of MCMC reps after burnin" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	230
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	231 <!--Data file format-->
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	232 <param argument="NUMINDS" value="" type="integer" label="Number of diploid individuals in data file" help="or [N]"/>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	233 <param argument="NUMLOCI" value="" type="integer" label="Number of loci in data file" help="or [L]"/>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	234 <param argument="PLOIDY" value="2" type="integer" label="Ploidy of data" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	235 <param argument="MISSING" value="-9" type="integer" label="Value given to missing genotype data" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	236 <param argument="ONEROWPERIND" checked="False" type="boolean" label="Store data for individuals in a single line" truevalue="1" falsevalue="0" help=" E.g., for diploid data, this would mean that the two alleles for each locus are in consecutive order in the same row, rather than being arranged in the same column, in two consecutive rows "/>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	237
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	238
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	239 <param argument="LABEL" checked="true" type="boolean" label="Input file contains individual labels" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	240 <param argument="POPDATA" checked="true" type="boolean" label="Input file contains a user-defined population-of-origin for each individual" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	241 <param argument="LOCDATA" checked="false" type="boolean" label="Input file contains a location identifier" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	242
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	243 <param argument="PHENOTYPE" checked="false" type="boolean" label="Input file contains phenotype information" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	244 <param argument="EXTRACOLS" value="0" type="integer" label="Number of additional columns of data before the genotype data start." />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	245
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	246 <param argument="MARKERNAMES" checked="true" type="boolean" label="Data file contains row of marker names" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	247 <conditional name="recessivealleles_cond">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	248 <param argument="RECESSIVEALLELES" type="select" label="Data file contains dominant markers (eg AFLPs) and a row to indicate which alleles are recessive" >
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	249 <option value="0" selected="True">No</option>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	250 <option value="1">Yes</option>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	251 </param>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	252 <when value="0">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	253 <param argument="NOTAMBIGUOUS" value="-999" type="hidden" label="Defines the code indicating that genotype data at a marker are unambiguous." help="For use with polyploids when RECESSIVEALLELES=1/True. Must not match MISSING or any allele value in the data." />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	254 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	255 <when value="1">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	256 <param argument="NOTAMBIGUOUS" value="-999" type="integer" label="Defines the code indicating that genotype data at a marker are unambiguous." help="For use with polyploids when RECESSIVEALLELES=1/True. Must not match MISSING or any allele value in the data." />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	257 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	258 </conditional>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	259 <param argument="MAPDISTANCES" checked="false" type="boolean" label="Data file contains row of map distances between loci" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	260
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	261
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	262 <!--Advanced data file options-->
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	263
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	264 <param argument="PHASED" checked="false" type="boolean" label="Data are in correct phase (relevant for linkage model only)" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	265 <param argument="PHASEINFO" checked="false" type="boolean" label="The data for each individual contains a line indicating phase (linkage model)" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	266 <param argument="MARKOVPHASE" checked="false" type="boolean" label="The phase info follows a Markov model." truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	267 </section>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	268 <section name="extra" title="extraparams" expanded="False">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	269
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	270 <param argument="NOADMIX" checked="false" type="boolean" label="Use no admixture model" help="(0/False=admixture model, 1/True=no-admix)" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	271 <param argument="LINKAGE" checked="false" type="boolean" label="Use the linkage model model" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	272 <conditional name="usepopinfo_cond">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	273 <param argument="USEPOPINFO" type="select" label="Use prior population information to pre-assign individuals to clusters">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	274 <option value="0" selected="True">No</option>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	275 <option value="1">Yes</option>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	276 </param>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	277 <when value="0">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	278 <param argument="POPFLAG" value="0" type="hidden" label="Input file contains a flag which says whether to use popinfo" help="[mainparams] when USEPOPINFO is 1/True" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	279 <param argument="MIGRPRIOR" value="0.01" type="hidden" label="Prior prob that an individual is a migrant" help="(used only when USEPOPINFO==1/True). This should be small, eg 0.01 or 0.1." />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	280 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	281 <when value="1">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	282 <param argument="POPFLAG" checked="false" type="boolean" label="Input file contains a flag which says whether to use popinfo" help="[mainparams] when USEPOPINFO is 1/True" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	283 <param argument="MIGRPRIOR" value="0.01" type="float" label="Prior prob that an individual is a migrant" help="(used only when USEPOPINFO==1/True). This should be small, eg 0.01 or 0.1." />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	284 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	285 </conditional>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	286 <param argument="LOCPRIOR" checked="false" type="boolean" label="Use location information to improve weak data" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	287
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	288 <param argument="FREQSCORR" checked="true" type="boolean" label="Allele frequencies are correlated among pops" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	289 <param argument="ONEFST" checked="false" type="boolean" label="Assume same value of Fst for all subpopulations" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	290
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	291 <conditional name="inferalpha_cond">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	292 <param argument="INFERALPHA" type="select" label="Infer ALPHA (the admixture parameter)">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	293 <option value="1" selected="True">Yes</option>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	294 <option value="0">No</option>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	295 </param>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	296 <when value="1">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	297 <param argument="ALPHA" value="1.0" type="float" label="Dirichlet parameter for degree of admixture" help="this is the initial value if INFERALPHA is 1/True." />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	298 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	299 <when value="0">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	300 <param argument="ALPHA" value="1.0" type="hidden" label="Dirichlet parameter for degree of admixture" help="this is the initial value if INFERALPHA is 1/True." />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	301 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	302 </conditional>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	303 <param argument="POPALPHAS" checked="false" type="boolean" label="Individual alpha for each population" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	304
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	305 <conditional name="inferlambda_cond">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	306 <param argument="INFERLAMBDA" type="select" label="Infer LAMBDA (the allele frequencies parameter)">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	307 <option value="0" selected="True">No</option>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	308 <option value="1">Yes</option>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	309 </param>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	310 <when value="0">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	311 <param argument="POPSPECIFICLAMBDA" value="0" type="hidden" label="Infer a separate lambda for each pop" help="(only if INFERLAMBDA=1/True)." />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	312 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	313 <when value="1">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	314 <param argument="POPSPECIFICLAMBDA" checked="false" type="boolean" label="Infer a separate lambda for each pop" help="(only if INFERLAMBDA=1/True)." truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	315 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	316 </conditional>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	317 <param argument="LAMBDA" value="1.0" type="float" label="Dirichlet parameter for allele frequencies" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	318
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	319
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	320 <!-- PRIORS -->
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	321
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	322 <param argument="FPRIORMEAN" value="0.01" type="float" label="The Prior (Gamma distribution) mean of Fst for pops." />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	323 <param argument="FPRIORSD" value="0.05" type="float" label="The Prior (Gamma distribution) Standard Deviation of Fst for pops." />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	324
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	325 <conditional name="unifprioralpha_cond">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	326 <param argument="UNIFPRIORALPHA" type="select" label="Use a uniform prior for alpha; otherwise gamma prior">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	327 <option value="1" selected="True">Yes</option>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	328 <option value="0">No</option>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	329 </param>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	330 <when value="1">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	331 <param argument="ALPHAPRIORA" value="1.0" type="hidden" label="Alpha has a gamma prior with mean AB, and variance AB^2." help="(only if UNIFPRIORALPHA==0/False)" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	332 <param argument="ALPHAPRIORB" value="2.0" type="hidden" label="Alpha has a gamma prior with mean AB, and variance AB^2." help="(only if UNIFPRIORALPHA==0/False)" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	333 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	334 <when value="0">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	335 <param argument="ALPHAPRIORA" value="1.0" type="float" label="Alpha has a gamma prior with mean AB, and variance AB^2." help="(only if UNIFPRIORALPHA==0/False)"/>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	336 <param argument="ALPHAPRIORB" value="2.0" type="float" label="Alpha has a gamma prior with mean AB, and variance AB^2." help="(only if UNIFPRIORALPHA==0/False)"/>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	337 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	338 </conditional>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	339 <param argument="ALPHAMAX" value="10.0" type="float" label="Max value of alpha if uniform prior" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	340
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	341
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	342 <param argument="LOG10RMIN" value="-4.0" type="float" label="Log10 of minimum allowed value of r under linkage model" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	343 <param argument="LOG10RMAX" value="1.0" type="float" label="Log10 of maximum allowed value of r" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	344 <param argument="LOG10RPROPSD" value="0.1" type="float" label="Standard deviation of log r in update" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	345 <param argument="LOG10RSTART" value="-2.0" type="float" label="Initial value of log10 r" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	346
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	347
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	348 <!-- USING PRIOR POPULATION INFO (USEPOPINFO) -->
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	349
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	350 <param argument="GENSBACK" value="2" type="integer" label="For use when inferring whether an individual is an immigrant, or has an immigrant an cestor in the past GENSBACK generations." help="eg, if GENSBACK==2, it tests for immigrant ancestry back to grandparents." />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	351 <param argument="PFROMPOPFLAGONLY" checked="false" type="boolean" label="Only use individuals with POPFLAG=1 to update P." help="This is to enable use of a reference set of individuals for clustering additional 'test' individuals." truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	352
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	353 <!-- LOCPRIOR MODEL FOR USING LOCATION INFORMATION -->
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	354
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	355 <param argument="LOCISPOP" checked="true" type="boolean" label="Use POPDATA for location information" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	356 <param argument="LOCPRIORINIT" value="1.0" type="float" label="Initial value for r, the location prior" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	357 <param argument="MAXLOCPRIOR" value="20.0" type="float" label="Max allowed value for r" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	358
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	359 <!-- OUTPUT OPTIONS -->
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	360
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	361 <param argument="PRINTNET" checked="true" type="boolean" label="Print the 'net nucleotide distance' to screen during the run" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	362 <param argument="PRINTLAMBDA" checked="true" type="boolean" label="Print current value(s) of lambda to screen" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	363 <param argument="PRINTQSUM" checked="true" type="boolean" label="Print summary of current population membership to screen" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	364
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	365 <param argument="SITEBYSITE" checked="false" type="boolean" label="whether or not to print site by site results." help="(Linkage model only) This is a large file!" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	366 <param argument="PRINTQHAT" checked="false" type="boolean" label="Q-hat printed to a separate file." help="Turn this on before using STRAT." truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	367 <param argument="UPDATEFREQ" value="100" type="integer" label="Frequency of printing update on the screen." help="Set automatically if this is 0/False." />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	368 <param argument="PRINTLIKES" checked="false" type="boolean" label="Print current likelihood to screen every rep" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	369 <param argument="INTERMEDSAVE" value="0" type="integer" label="Number of saves to file during run" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	370
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	371 <param argument="ECHODATA" checked="false" type="boolean" label="Print some of data file to screen to check that the data entry is correct." help="(NEXT 3 ARE FOR COLLECTING DISTRIBUTION OF Q:)" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	372 <param argument="ANCESTDIST" checked="false" type="boolean" label="Collect data about the distribution of ancestry coefficients (Q) for each individual" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	373 <param argument="NUMBOXES" value="1000" type="integer" label="The distribution of Q values is stored as a histogram with this number of boxes." />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	374 <param argument="ANCESTPINT" value="0.90" type="float" label="The size of the displayed probability interval on Q (values between 0.0--1.0)" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	375
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	376
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	377
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	378 <!-- MISCELLANEOUS -->
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	379
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	380 <param argument="COMPUTEPROB" checked="true" type="boolean" label="Estimate the probability of the Data under the model." help="This is used when choosing the best number of subpopulations." truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	381 <param argument="ADMBURNIN" value="500" type="integer" label="Initial period of burnin with admixture model" help="[only relevant for linkage model] see Documentation" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	382 <param argument="ALPHAPROPSD" value="0.025" type="float" label="SD of proposal for updating alpha" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	383 <param argument="STARTATPOPINFO" checked="false" type="boolean" label="Use given populations as the initial condition for population origins." help="(Need POPDATA==1). It is assumed that the PopData in the input file are between 1 and k where k is less or equal MAXPOPS." truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	384 <conditional name="randomize_cond">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	385 <param argument="RANDOMIZE" type="select" label="=use new random seed for each run">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	386 <option value="1" selected="True">Yes</option>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	387 <option value="0">No</option>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	388 </param>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	389 <when value="1">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	390 <param argument="SEED" value="2245" type="hidden" label="Seed value for random number generator" help="(must set RANDOMIZE=0)" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	391 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	392 <when value="0">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	393 <param argument="SEED" value="2245" type="integer" label="seed value for random number generator" help="(must set RANDOMIZE=0)" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	394 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	395 </conditional>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	396 <param argument="METROFREQ" value="10" type="integer" label="Frequency of using Metropolis step to update Q under admixture model" help="(ie use the metr. move every i steps). If this is set to 0, it is never used. (Proposal for each q^(i) sampled from prior. The goal is to improve mixing for small alpha.)" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	397 <param argument="REPORTHITRATE" checked="false" type="boolean" label="Report hit rate if using METROFREQ" truevalue="1" falsevalue="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	398 </section>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	399 </inputs>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	400 <outputs>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	401 <data name="out_mainparams" format="txt" label="run_K_${main.MAXPOPS}.mainparams" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	402 <data name="out_extraparams" format="txt" label="run_K_${main.MAXPOPS}.extraparams" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	403 <collection name="out" type="list" label="run_K_${main.MAXPOPS}.out">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	404 <discover_datasets pattern="__name__" format="tabular" directory="out" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	405 </collection>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	406 <collection name="log" type="list" label="run_K_${main.MAXPOPS}.log">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	407 <discover_datasets pattern="__name__" format="tabular" directory="log" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	408 </collection>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	409 </outputs>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	410 <tests>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	411 <test>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	412 <!-- https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/html/structure-data.html -->
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	413 <param name="infile" value="testdata1" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	414 <param name="nb_run" value="2" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	415 <section name="main">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	416 <param name="NUMINDS" value="200" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	417 <param name="MAXPOPS" value="2" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	418 <param name="LABEL" value="1" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	419 <param name="POPDATA" value="1" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	420 <param name="NUMLOCI" value="5" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	421 <param name="LOCDATA" value="1" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	422 <param name="PLOIDY" value="2" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	423 <param name="MISSING" value="-999" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	424 <param name="ONEROWPERIND" value="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	425 <param name="MARKERNAMES" value="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	426 </section>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	427 <section name="extra">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	428 <conditional name="randomize_cond">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	429 <param name="RANDOMIZE" value="0" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	430 </conditional>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	431 </section>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	432 <output_collection name="out" type="list">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	433 <element name="run1_K_2.out" value="testdata1_f" lines_diff="6" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	434 <element name="run2_K_2.out" value="testdata1_f" lines_diff="6" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	435 </output_collection>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	436 <output_collection name="log" type="list">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	437 <element name="run1_K_2.log">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	438 <assert_contents>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	439 <has_line line="Final results printed to file outfile_f" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	440 </assert_contents>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	441 </element>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	442 <element name="run2_K_2.log">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	443 <assert_contents>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	444 <has_line line="Final results printed to file outfile_f" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	445 </assert_contents>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	446 </element>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	447 </output_collection>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	448 </test>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	449 </tests>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	450 <help><![CDATA[
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	451 Introduction
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	452
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	453 The program structure_ implements a model-based clustering method for inferring population structure
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	454 using genotype data consisting of unlinked markers. The method was introduced in a paper
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	455 by Pritchard, Stephens and Donnelly (2000a) and extended in sequels by Falush, Stephens and
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	456 Pritchard (2003a, 2007). Applications of our method include demonstrating the presence of population
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	457 structure, identifying distinct genetic populations, assigning individuals to populations, and
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	458 identifying migrants and admixed individuals.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	459
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	460 Briefly, we assume a model in which there are K populations (where K may be unknown),
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	461 each of which is characterized by a set of allele frequencies at each locus. Individuals in the
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	462 sample are assigned (probabilistically) to populations, or jointly to two or more populations if their
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	463 genotypes indicate that they are admixed. It is assumed that within populations, the loci are at
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	464 Hardy-Weinberg equilibrium, and linkage equilibrium. Loosely speaking, individuals are assigned
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	465 to populations in such a way as to achieve this.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	466
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	467 Our model does not assume a particular mutation process, and it can be applied to most of the
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	468 commonly used genetic markers including microsatellites, SNPs and RFLPs. The model assumes
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	469 that markers are not in linkage disequilibrium (LD) within subpopulations, so we can’t handle
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	470 markers that are extremely close together. Starting with version 2.0, we can now deal with weakly
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	471 linked markers.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	472
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	473 While the computational approaches implemented here are fairly powerful, some care is needed
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	474 in running the program in order to ensure sensible answers. For example, it is not possible to
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	475 determine suitable run-lengths theoretically, and this requires some experimentation on the part of
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	476 the user. This document describes the use and interpretation of the software and supplements the
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	477 published papers, which provide more formal descriptions and evaluations of the methods.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	478
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	479 .. _structure: https://web.stanford.edu/group/pritchardlab/structure.html
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	480
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	481 Documentation
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	482
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	483 Please see the full Sructure documentation_
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	484
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	485 .. _documentation: https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/structure_doc.pdf
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	486
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	487 Upstream
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	488
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	489 Inputs can be produced from:
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	490
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	491 - Microsatellite analysis
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	492 - RADSeq analysis (eg: using populations_ from Stacks suite)
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	493
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	494 .. _populations: http://catchenlab.life.illinois.edu/stacks/manual/#export
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	495
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	496 Input
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	497
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	498 ======= === ===== ===== ===== ===== =====
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	499 loc_a loc_b loc_c loc_d loc_e
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	500 ======= === ===== ===== ===== ===== =====
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	501 George 1 -9 145 66 0 92
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	502 George 1 -9 -9 64 0 94
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	503 Paula 1 106 142 68 1 92
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	504 Paula 1 106 148 64 0 94
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	505 Matthew 2 110 145 -9 0 92
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	506 Matthew 2 110 148 66 1 -9
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	507 Bob 2 108 142 64 1 94
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	508 Bob 2 -9 142 -9 0 94
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	509 Anja 1 112 142 -9 1 -9
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	510 Anja 1 114 142 66 1 94
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	511 Peter 1 -9 145 66 0 -9
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	512 Peter 1 110 145 -9 1 -9
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	513 Carsten 2 108 145 62 0 -9
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	514 Carsten 2 110 145 64 1 92
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	515 ======= === ===== ===== ===== ===== =====
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	516
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	517 You will find other sample data sets: here_
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	518
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	519 .. _here: https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/html/structure-data.html
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	520
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	521 Downstream
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	522
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	523 - Clumpp_
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	524 - Distruct_
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	525 - Structure-harvester_
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	526
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	527 .. _Clumpp: https://rosenberglab.stanford.edu/clumpp.html
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	528 .. _Distruct: https://rosenberglab.stanford.edu/distruct.html
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	529 .. _Structure-harvester: http://taylor0.biology.ucla.edu/structureHarvester/
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	530
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	531 ]]></help>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	532 <citations>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	533 <citation type="doi">10.1111/j.1471-8286.2007.01758.x</citation>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	534 <citation type="doi">10.1111/j.1755-0998.2009.02591.x</citation>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	535 </citations>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	536 </tool>

Mercurial > repos > iuc > structure

annotate structure.xml @ 0:a1574aada200 draft