structure: structure.xml annotate

annotate structure.xml @ 3:4bd5e5dbc6c5 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit f03b7df7b3e4fd099ae0e1bd195c41ab2e0fa227"

author	iuc
date	Sun, 20 Mar 2022 10:57:34 +0000
parents	0080ad37f8a0
children

rev	line source
3 4bd5e5dbc6c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit f03b7df7b3e4fd099ae0e1bd195c41ab2e0fa227" iuc parents: 2 diff changeset	1 <tool id="structure" name="Structure" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
0 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>
3 4bd5e5dbc6c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit f03b7df7b3e4fd099ae0e1bd195c41ab2e0fa227" iuc parents: 2 diff changeset	3 <xrefs>
4bd5e5dbc6c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit f03b7df7b3e4fd099ae0e1bd195c41ab2e0fa227" iuc parents: 2 diff changeset	4 <xref type="bio.tools">structure</xref>
4bd5e5dbc6c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit f03b7df7b3e4fd099ae0e1bd195c41ab2e0fa227" iuc parents: 2 diff changeset	5 </xrefs>
4bd5e5dbc6c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit f03b7df7b3e4fd099ae0e1bd195c41ab2e0fa227" iuc parents: 2 diff changeset	6 <macros>
4bd5e5dbc6c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit f03b7df7b3e4fd099ae0e1bd195c41ab2e0fa227" iuc parents: 2 diff changeset	7 <token name="@TOOL_VERSION@">2.3.4</token>
4bd5e5dbc6c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit f03b7df7b3e4fd099ae0e1bd195c41ab2e0fa227" iuc parents: 2 diff changeset	8 <token name="@VERSION_SUFFIX@">1</token>
4bd5e5dbc6c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit f03b7df7b3e4fd099ae0e1bd195c41ab2e0fa227" iuc parents: 2 diff changeset	9 </macros>
0 a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	10 <requirements>
3 4bd5e5dbc6c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit f03b7df7b3e4fd099ae0e1bd195c41ab2e0fa227" iuc parents: 2 diff changeset	11 <requirement type="package" version="@TOOL_VERSION@">structure</requirement>
0 a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	12 </requirements>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	13 <version_command><![CDATA[
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	14 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	15 ]]></version_command>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	16 <command detect_errors="exit_code"><![CDATA[
3 4bd5e5dbc6c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit f03b7df7b3e4fd099ae0e1bd195c41ab2e0fa227" iuc parents: 2 diff changeset	17 cp '$mainparams' '$out_mainparams' &&
4bd5e5dbc6c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit f03b7df7b3e4fd099ae0e1bd195c41ab2e0fa227" iuc parents: 2 diff changeset	18 cp '$extraparams' '$out_extraparams' &&
0 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 mkdir out log
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	21
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	22 #for $run in range(1, int($nb_run) + 1):
2 0080ad37f8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit 23755ec4deed7de2d80bfb7de30e0bfc2eaa3818 iuc parents: 1 diff changeset	23 && structure -i '$infile' -o outfile -m '$out_mainparams' -e '$out_extraparams' > 'log/K_${main.MAXPOPS}_run_${run}_f.log'
0080ad37f8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit 23755ec4deed7de2d80bfb7de30e0bfc2eaa3818 iuc parents: 1 diff changeset	24 && mv 'outfile_f' 'out/K_${main.MAXPOPS}_run_${run}_f'
0 a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	25 #end for
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 ]]></command>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	28 <configfiles>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	29 <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	30 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	31 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	32 FILE extraparams.
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
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	35 "(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	36 "(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	37 (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	38 "(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	39
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	40
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	41 Basic Program Parameters
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	42
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	43 #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	44 #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	45 #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	46
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	47 Input/Output files
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	48
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	49 #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	50 #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	51
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	52 Data file format
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 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	55 #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	56 #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	57 #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	58 #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	59
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	60
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	61 #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	62 #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	63 #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	64 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	65 #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	66
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	67 #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	68 #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	69 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	70
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	71 #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	72 #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	73 // 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	74 #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	75 // between loci
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	76
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	77
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	78 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	79
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	80 #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	81 #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	82 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	83 #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	84 #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	85
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	86
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	87
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	88 Command line options:
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	89
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	90 -m mainparams
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	91 -e extraparams
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	92 -s stratparams
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	93 -K MAXPOPS
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	94 -L NUMLOCI
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	95 -N NUMINDS
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	96 -i input file
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	97 -o output file
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	98 -D SEED
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	99
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	100 ]]></configfile>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	101 <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	102 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	103 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	104 SPECIFIED IN mainparams.
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 "(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	107 "(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	108 "(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	109 (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	110
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	111 PROGRAM OPTIONS
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	112
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	113 #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	114 #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	115 #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	116 to clusters
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	117 #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	118
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	119 #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	120 #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	121
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	122 #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	123 #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	124 #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	125 (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	126
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	127 #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	128 #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	129 (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	130 #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	131
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
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	134
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	135 PRIORS
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	136
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	137 #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	138 #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	139
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	140 #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	141 otherwise gamma prior
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	142 #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	143 #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	144 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	145 #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	146
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	147
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	148 #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	149 #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	150 #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	151 #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	152
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	153
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	154 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	155
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	156 #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	157 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	158 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	159 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	160 back to grandparents.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	161 #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	162 (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	163 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	164 #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	165 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	166 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	167 individuals.
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 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	170
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	171 #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	172 #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	173 #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	174
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	175
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
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	178 OUTPUT OPTIONS
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	179
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	180 #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	181 #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	182 #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	183
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	184 #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	185 (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	186 #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	187 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	188 #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	189 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	190 #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	191 #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	192
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	193 #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	194 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	195 (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	196 #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	197 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	198 #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	199 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	200 #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	201 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	202
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	203
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	204
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	205 MISCELLANEOUS
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	206
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	207 #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	208 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	209 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	210 #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	211 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	212 #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	213 #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	214 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	215 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	216 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	217 #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	218 #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	219 (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	220 #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	221 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	222 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	223 (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	224 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	225 #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	226
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	227 ]]></configfile>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	228 </configfiles>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	229 <inputs>
3 4bd5e5dbc6c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit f03b7df7b3e4fd099ae0e1bd195c41ab2e0fa227" iuc parents: 2 diff changeset	230 <param name="infile" type="data" label="Genotype data" format="txt,tabular" />
0 a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	231 <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	232 <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	233 <!--Basic Program Parameters-->
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	234 <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	235 <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	236 <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	237
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	238 <!--Data file format-->
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	239 <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	240 <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	241 <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	242 <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	243 <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	244
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="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	247 <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	248 <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	249
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	250 <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	251 <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	252
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	253 <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	254 <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	255 <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	256 <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	257 <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	258 </param>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	259 <when value="0">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	260 <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	261 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	262 <when value="1">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	263 <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	264 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	265 </conditional>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	266 <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	267
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	268
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	269 <!--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	270
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	271 <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	272 <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	273 <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	274 </section>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	275 <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	276
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	277 <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	278 <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	279 <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	280 <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	281 <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	282 <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	283 </param>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	284 <when value="0">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	285 <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	286 <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	287 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	288 <when value="1">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	289 <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	290 <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	291 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	292 </conditional>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	293 <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	294
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	295 <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	296 <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	297
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	298 <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	299 <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	300 <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	301 <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	302 </param>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	303 <when value="1">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	304 <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	305 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	306 <when value="0">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	307 <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	308 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	309 </conditional>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	310 <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	311
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	312 <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	313 <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	314 <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	315 <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	316 </param>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	317 <when value="0">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	318 <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	319 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	320 <when value="1">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	321 <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	322 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	323 </conditional>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	324 <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	325
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	326
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	327 <!-- PRIORS -->
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	328
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	329 <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	330 <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	331
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	332 <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	333 <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	334 <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	335 <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	336 </param>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	337 <when value="1">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	338 <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	339 <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	340 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	341 <when value="0">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	342 <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	343 <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	344 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	345 </conditional>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	346 <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	347
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	348
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	349 <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	350 <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	351 <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	352 <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	353
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 <!-- 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	356
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	357 <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	358 <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	359
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	360 <!-- 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	361
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	362 <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	363 <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	364 <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	365
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	366 <!-- OUTPUT OPTIONS -->
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	367
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	368 <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	369 <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	370 <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	371
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	372 <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	373 <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	374 <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	375 <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	376 <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	377
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	378 <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	379 <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	380 <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	381 <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	382
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	383
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	384
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	385 <!-- MISCELLANEOUS -->
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	386
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	387 <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	388 <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	389 <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	390 <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	391 <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	392 <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	393 <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	394 <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	395 </param>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	396 <when value="1">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	397 <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	398 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	399 <when value="0">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	400 <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	401 </when>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	402 </conditional>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	403 <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	404 <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	405 </section>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	406 </inputs>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	407 <outputs>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	408 <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	409 <data name="out_extraparams" format="txt" label="run_K_${main.MAXPOPS}.extraparams" />
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	410 <collection name="out" type="list" label="run_K_${main.MAXPOPS}.out">
1 64e681a1cad5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit 5294b1b0cf9d347a0f7982ae6b0fa357d0198898 iuc parents: 0 diff changeset	411 <discover_datasets pattern="__name__" format="txt" directory="out" />
0 a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	412 </collection>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	413 <collection name="log" type="list" label="run_K_${main.MAXPOPS}.log">
1 64e681a1cad5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit 5294b1b0cf9d347a0f7982ae6b0fa357d0198898 iuc parents: 0 diff changeset	414 <discover_datasets pattern="__name__" format="txt" directory="log" />
0 a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	415 </collection>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	416 </outputs>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	417 <tests>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	418 <test>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	419 <!-- 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	420 <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	421 <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	422 <section name="main">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	423 <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	424 <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	425 <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	426 <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	427 <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	428 <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	429 <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	430 <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	431 <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	432 <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	433 </section>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	434 <section name="extra">
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	435 <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	436 <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	437 </conditional>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	438 </section>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	439 <output_collection name="out" type="list">
2 0080ad37f8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit 23755ec4deed7de2d80bfb7de30e0bfc2eaa3818 iuc parents: 1 diff changeset	440 <element name="K_2_run_1_f" value="testdata1_f" lines_diff="6" />
0080ad37f8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit 23755ec4deed7de2d80bfb7de30e0bfc2eaa3818 iuc parents: 1 diff changeset	441 <element name="K_2_run_2_f" value="testdata1_f" lines_diff="6" />
0 a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	442 </output_collection>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	443 <output_collection name="log" type="list">
2 0080ad37f8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit 23755ec4deed7de2d80bfb7de30e0bfc2eaa3818 iuc parents: 1 diff changeset	444 <element name="K_2_run_1_f.log">
0 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 <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	447 </assert_contents>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	448 </element>
2 0080ad37f8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit 23755ec4deed7de2d80bfb7de30e0bfc2eaa3818 iuc parents: 1 diff changeset	449 <element name="K_2_run_2_f.log">
0 a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	450 <assert_contents>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	451 <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	452 </assert_contents>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	453 </element>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	454 </output_collection>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	455 </test>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	456 </tests>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	457 <help><![CDATA[
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	458 Introduction
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 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	461 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	462 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	463 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	464 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	465 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	466
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	467 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	468 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	469 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	470 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	471 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	472 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	473
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	474 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	475 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	476 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	477 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	478 linked markers.
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	479
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	480 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	481 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	482 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	483 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	484 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	485
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	486 .. _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	487
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	488 Documentation
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	489
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	490 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	491
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	492 .. _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	493
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	494 Upstream
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 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	497
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	498 - Microsatellite analysis
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	499 - 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	500
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	501 .. _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	502
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	503 Input
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	504
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	505 ======= === ===== ===== ===== ===== =====
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	506 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	507 ======= === ===== ===== ===== ===== =====
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	508 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	509 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	510 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	511 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	512 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	513 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	514 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	515 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	516 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	517 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	518 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	519 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	520 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	521 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	522 ======= === ===== ===== ===== ===== =====
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	523
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	524 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	525
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	526 .. _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	527
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	528 Downstream
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	529
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	530 - Clumpp_
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	531 - Distruct_
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	532 - Structure-harvester_
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	533
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	534 .. _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	535 .. _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	536 .. _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	537
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	538 ]]></help>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	539 <citations>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	540 <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	541 <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	542 </citations>
a1574aada200 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit b4d0a8f3dfee920840c77befdf626c52a5d617cb iuc parents: diff changeset	543 </tool>

Mercurial > repos > iuc > structure

annotate structure.xml @ 3:4bd5e5dbc6c5 draft default tip