--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/admixture/Admixture.pl	Fri Feb 20 10:11:57 2015 -0500
@@ -0,0 +1,159 @@
+#!/usr/bin/perl
+
+use strict;
+use Switch;
+use Getopt::Long;
+use Bio::SeqIO;
+
+my $usage = qq~Usage:$0 <args> [<opts>]
+where <args> are:
+    -i, --input         <input HAPMAP>
+    -o, --output        <output>
+    -k, --kmin          <K min. int>
+    -m, --maxK          <K max. int>
+    -d, --directory     <temporary directory>
+    -p, --path          <path to executables>
+~;
+$usage .= "\n";
+
+my ($input,$output,$kmin,$kmax,$directory,$path);
+
+
+GetOptions(
+	"input=s"      => \$input,
+	"output=s"     => \$output,
+	"kmin=s"       => \$kmin,
+	"maxK=s"       => \$kmax,
+	"directory=s"  => \$directory,
+	"path=s"       => \$path
+);
+
+
+die $usage
+  if ( !$input || !$output || !$kmin || !$kmax || !$directory || !$path);
+
+if ($kmin =~/^(\d+)\s*$/){
+        $kmin = $1;
+}
+else{
+        die "Error: kmin must be an integer\n";
+}
+if ($kmax =~/^(\d+)\s*$/){
+        $kmax = $1;
+}
+else{
+        die "Error: kmax must be an integer\n";
+}
+
+  
+######################
+# create map file
+######################
+open(my $M,">$directory/input.map");
+open(my $H,$input);
+<$H>;
+while(<$H>)
+{
+	my @infos = split(/\t/,$_);
+	print $M $infos[2] . "\t" . $infos[0] . "\t" . "0" . "\t" . $infos[3] . "\n";
+}
+close($H);
+close($M);
+
+######################
+# create ped file
+######################
+system("$path/transpose.awk $input >$directory/input.ped.2");
+
+open(my $P,">$directory/input.ped");
+open(my $P2,"$directory/input.ped.2");
+my $n = 0;
+my $ind_num = 0;
+my @individus;
+while(<$P2>)
+{
+	$n++;
+	if ($n > 11)
+	{
+		my $line = $_;
+		$line =~s/N/0/g;
+		if (/^([^\s]+)\s+(.*)$/)
+		{
+			$ind_num++;
+			my $ind = $1;
+			push(@individus,$ind);
+			my $genoyping_line = $2;
+			print $P "$ind	$ind_num	0	0	1	2";
+			my @genotypes = split(/\s/,$genoyping_line);
+			foreach my $genotype(@genotypes)
+			{
+				$genotype =~s/N/0/g;
+				my @alleles = split("",$genotype);
+				print $P "	" . join(" ",@alleles);
+			}
+			
+			print $P "\n";
+		}
+	}
+}
+close($P2);
+close($P);
+
+unlink("$directory/input.ped.2");
+
+system("plink --file $directory/input --out $directory/out --make-bed --noweb >>$directory/plink.log 2>&1");
+
+
+###################################
+# launch admixture for different K
+###################################
+my %errors;
+for (my $k = $kmin; $k <= $kmax; $k++)
+{
+	system("admixture --cv $directory/out.bed $k >>$directory/log.$k 2>&1");
+	my $cv_error_line = `grep -h CV $directory/log.$k`;
+	if ($cv_error_line =~/: (\d+\.*\d*)$/)
+	{
+		$errors{$1} = $k;
+	}
+	system("cat $directory/log.$k >>$directory/logs");
+	system("echo '\n\n====================================\n\n' >>$directory/logs");
+	system("cat out.$k.Q >>$directory/outputs.Q");
+	system("echo '\n\n====================================\n\n' >>$directory/outputs.Q");
+	system("cat out.$k.P >>$directory/outputs.P");
+	system("echo '\n\n====================================\n\n' >>$directory/outputs.P");
+}
+
+my @sorted_errors = sort {$a<=>$b} keys(%errors);
+my $best_K = $errors{@sorted_errors[0]};
+
+
+#system("cp -rf out.$best_K.Q $directory/output");
+
+open(BEST1,"out.$best_K.Q");
+open(BEST2,">$directory/output");
+print BEST2 "<Covariate>\n";
+print BEST2 "<Trait>";
+for (my $j=1;$j<=$best_K;$j++)
+{
+	print BEST2 "	Q" . $j;
+}
+print BEST2 "\n";
+my $i = 0;
+while(<BEST1>)
+{
+	my $line = $_;
+	$line =~s/ /\t/g;
+	my $ind = $individus[$i];
+	print BEST2 "$ind	";
+	print BEST2 $line;
+	$i++;
+}
+close(BEST1);
+close(BEST2);
+
+system("cp -rf $directory/log.$best_K $directory/log");
+
+
+
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/admixture/admixture.sh	Fri Feb 20 10:11:57 2015 -0500
@@ -0,0 +1,21 @@
+#!/bin/bash
+input=$1
+outputs=$2
+logs=$3
+best_k_output=$4
+best_k_logfile=$5
+kmin=$6
+kmax=$7
+
+directory=`dirname $0`
+mkdir tmpdir$$
+cp -rf $input tmpdir$$/input
+ 
+/usr/bin/perl $directory/Admixture.pl -i $input -o $outputs -k $kmin -m $kmax -d tmpdir$$ -p $directory
+
+mv tmpdir$$/output $best_k_output
+mv tmpdir$$/log $best_k_logfile
+mv tmpdir$$/outputs.Q $outputs
+mv tmpdir$$/logs $logs
+
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/admixture/admixture.xml	Fri Feb 20 10:11:57 2015 -0500
@@ -0,0 +1,55 @@
+<tool id="admixture" name="Admixture" version="1.23">
+	<description>a population structure from large SNP genotype datasets</description>
+	<requirements>
+		<requirement type="package" version="1.07">plink</requirement>
+		<requirement type="package" version="1.23">admixture</requirement>
+	</requirements>
+	<command interpreter="bash">./admixture.sh $input $outputs $logs $best_k_output $best_k_logfile $kmin $kmax
+    </command>
+	<inputs>
+		<param format="txt" name="input" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/>
+		<param type="text" name="kmin" label="K min" value="1"/>
+		<param type="text" name="kmax" label="K max" value="5"/>
+	</inputs>
+	<outputs>
+		<data format="txt" name="best_k_output" label="Best K Output"/>
+		<data format="txt" name="best_k_logfile" label="Best K Logfile"/>
+		<data format="txt" name="outputs" label="All Outputs"/>
+		<data format="txt" name="logs" label="All Logs"/>
+	</outputs>
+	<help>
+	
+
+.. class:: infomark
+
+**Program encapsulated in Galaxy by Southgreen**
+
+.. class:: infomark
+
+**Admixture version 1.23**
+
+-----
+
+==============
+ Please cite: 
+==============
+
+"Fast model-based estimation of ancestry in unrelated individuals.", **D.H. Alexander, J. Novembre, and K. Lange.**, Genome Research, 19:1655{1664, 2009.
+
+-----
+
+===========
+ Overview:
+===========
+
+ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study).
+
+-----
+
+For further informations, please visite the Admixture_ website.
+
+
+.. _Admixture: http://www.genetics.ucla.edu/software/admixture/index.html
+	</help>
+
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/admixture/tool-data/tool_dependencies.xml	Fri Feb 20 10:11:57 2015 -0500
@@ -0,0 +1,11 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="plink" version="1.07">
+        <repository changeset_revision="65400c333b88" name="package_plink_1_07" owner="dereeper" toolshed="https://toolshed.g2.bx.psu.edu/" />
+    </package>
+    <package name="admixture" version="1.23">
+        <repository changeset_revision="61e04b2aa621" name="package_admixture_1_23" owner="dereeper" toolshed="https://toolshed.g2.bx.psu.edu/" />
+    </package>
+</tool_dependency>
+
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/admixture/transpose.awk	Fri Feb 20 10:11:57 2015 -0500
@@ -0,0 +1,27 @@
+#!/usr/bin/gawk -f
+
+BEGIN {
+    max_x =0;
+    max_y =0;
+}
+
+{
+    max_y++;
+    for( i=1; i<=NF; i++ )
+    {
+        if (i>max_x) max_x=i;
+        A[i,max_y] = $i;
+    }
+}
+
+END {
+    for ( x=1; x<=max_x; x++ )
+    {
+        for ( y=1; y<=max_y; y++ )
+        {
+            if ( (x,y) in A ) printf "%s",A[x,y];
+            if ( y!=max_y ) printf " ";
+        }
+        printf "\n";
+    }
+}