Mercurial > repos > dereeper > admixture
changeset 0:401a257d2792 draft
planemo upload
| author | dereeper |
|---|---|
| date | Tue, 12 Apr 2016 08:32:23 -0400 |
| parents | |
| children | bb126a88d0b3 |
| files | Admixture.pl admixture.sh admixture.xml test-data/input.bed test-data/input.bim test-data/input.fam test-data/output test-data/outputs.Q tool_dependencies.xml |
| diffstat | 9 files changed, 7389 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admixture.sh Tue Apr 12 08:32:23 2016 -0400 @@ -0,0 +1,26 @@ +#!/bin/bash +bed=$1 +fam=$2 +bim=$3 +outputs=$4 +logs=$5 +best_k_output=$6 +best_k_logfile=$7 +kmin=$8 +kmax=$9 + +directory=`dirname $0` +mkdir tmpdir$$ +cp -rf $bed tmpdir$$/input.bed +cp -rf $fam tmpdir$$/input.fam +cp -rf $bim tmpdir$$/input.bim + + +perl $directory/Admixture.pl -i tmpdir$$/input -o $outputs -k $kmin -m $kmax -d tmpdir$$ + +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.xml Tue Apr 12 08:32:23 2016 -0400 @@ -0,0 +1,77 @@ +<tool id="admixture" name="Admixture" version="1.23"> + <description>a population structure from large SNP genotype datasets</description> + <requirements> + <requirement type="package" version="1.23">admixture</requirement> + </requirements> + <command interpreter="bash">./admixture.sh $bed $fam $bim $outputs $logs $best_k_output $best_k_logfile $kmin $kmax + </command> + <inputs> + <param format="txt" name="bed" type="data" label="Allelic file in BED format" help="Allelic file in BED format"/> + <param format="txt" name="fam" type="data" label="Fam file" help="Fam file"/> + <param format="txt" name="bim" type="data" label="Bim file" help="Bim file"/> + <param type="text" name="kmin" label="K min" value="2"/> + <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> + + <tests> + <test> + <param name="bed" value="input.bed" /> + <param name="bim" value="input.bim" /> + <param name="fam" value="input.fam" /> + <param name="kmax" value="3" /> + + <output name="best_k_output" file="output" /> + <output name="outputs" file="outputs.Q" /> + </test> + + </tests> + + <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> + +<citations> +<citation type="doi" >10.1101/gr.094052.109</citation> +</citations> + + + +</tool>
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fam Tue Apr 12 08:32:23 2016 -0400 @@ -0,0 +1,167 @@ +AZUCENA AZUCENA 0 0 0 -9 +BULUPANDAK BULUPANDAK 0 0 0 -9 +GIZA171 GIZA171 0 0 0 -9 +IAC165 IAC165 0 0 0 -9 +KHAODAM KHAODAM 0 0 0 -9 +M202 M202 0 0 0 -9 +MOROBEREKAN MOROBEREKAN 0 0 0 -9 +NIPPONBARE_D NIPPONBARE_D 0 0 0 -9 +62667 62667 0 0 0 -9 +63-104 63-104 0 0 0 -9 +ARAGUAIA ARAGUAIA 0 0 0 -9 +ARIAS ARIAS 0 0 0 -9 +ARROZCEBADA ARROZCEBADA 0 0 0 -9 +BABER BABER 0 0 0 -9 +BAGANANASALAO BAGANANASALAO 0 0 0 -9 +BAKUNGH BAKUNGH 0 0 0 -9 +BENGALYVAKARINA BENGALYVAKARINA 0 0 0 -9 +BICOBRANCO BICOBRANCO 0 0 0 -9 +BINULAWAN BINULAWAN 0 0 0 -9 +CAAWA/FORTUNA6 CAAWA/FORTUNA6 0 0 0 -9 +CAIAPO CAIAPO 0 0 0 -9 +CANAROXA CANAROXA 0 0 0 -9 +CANELADEFERRO CANELADEFERRO 0 0 0 -9 +CHALOYOE CHALOYOE 0 0 0 -9 +CHAPHUMA CHAPHUMA 0 0 0 -9 +CICIHBETON CICIHBETON 0 0 0 -9 +CIRAD358 CIRAD358 0 0 0 -9 +CIRAD392 CIRAD392 0 0 0 -9 +CIRAD394 CIRAD394 0 0 0 -9 +CIRAD403 CIRAD403 0 0 0 -9 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IR63380-16 0 0 0 -9 +IR63372-08 IR63372-08 0 0 0 -9 +IR65907-188-1-B IR65907-188-1-B 0 0 0 -9 +IR66421-096-2-1-1 IR66421-096-2-1-1 0 0 0 -9 +IR68704-145-1-1-B IR68704-145-1-1-B 0 0 0 -9 +IR71525-19-1-1 IR71525-19-1-1 0 0 0 -9 +IRAT104 IRAT104 0 0 0 -9 +IRAT109 IRAT109 0 0 0 -9 +IRAT112 IRAT112 0 0 0 -9 +IRAT13 IRAT13 0 0 0 -9 +IRAT144 IRAT144 0 0 0 -9 +IRAT170 IRAT170 0 0 0 -9 +IRAT177 IRAT177 0 0 0 -9 +IRAT2 IRAT2 0 0 0 -9 +IRAT212 IRAT212 0 0 0 -9 +IRAT216 IRAT216 0 0 0 -9 +IRAT234 IRAT234 0 0 0 -9 +IRAT257 IRAT257 0 0 0 -9 +IRAT335 IRAT335 0 0 0 -9 +IRAT362 IRAT362 0 0 0 -9 +IRAT364 IRAT364 0 0 0 -9 +IRAT366 IRAT366 0 0 0 -9 +IRAT380 IRAT380 0 0 0 -9 +JAOHAW JAOHAW 0 0 0 -9 +JIMBRUKJOLOWORO JIMBRUKJOLOWORO 0 0 0 -9 +JUMALI JUMALI 0 0 0 -9 +JUMULA2 JUMULA2 0 0 0 -9 +KAKANI2 KAKANI2 0 0 0 -9 +KANIRANGA KANIRANGA 0 0 0 -9 +KARASUKARASURANKASU KARASUKARASURANKASU 0 0 0 -9 +KEDAYAN KEDAYAN 0 0 0 -9 +KENDINGA5H KENDINGA5H 0 0 0 -9 +KETANKONIR KETANKONIR 0 0 0 -9 +KETANLUMBU KETANLUMBU 0 0 0 -9 +KETANMENAH KETANMENAH 0 0 0 -9 +KHAOKAPXANG KHAOKAPXANG 0 0 0 -9 +KINANDANGPATONG KINANDANGPATONG 0 0 0 -9 +KOMOJAMANITRA KOMOJAMANITRA 0 0 0 -9 +KU115 KU115 0 0 0 -9 +KUROKA KUROKA 0 0 0 -9 +LAMBAYQUE1 LAMBAYQUE1 0 0 0 -9 +LUDAN LUDAN 0 0 0 -9 +MAHAE MAHAE 0 0 0 -9 +MAINTIMOLOTSY1226 MAINTIMOLOTSY1226 0 0 0 -9 +MALAGKITPIRURUTONG MALAGKITPIRURUTONG 0 0 0 -9 +MANANELATRA520 MANANELATRA520 0 0 0 -9 +MANDRIRAVINA3512 MANDRIRAVINA3512 0 0 0 -9 +MARAVILHA MARAVILHA 0 0 0 -9 +MITSANGANAHIJERY MITSANGANAHIJERY 0 0 0 -9 +MOLOK MOLOK 0 0 0 -9 +NABESHI NABESHI 0 0 0 -9 +NEPHOAVANG NEPHOAVANG 0 0 0 -9 +NHTA10 NHTA10 0 0 0 -9 +NHTA5 NHTA5 0 0 0 -9 +NPE253 NPE253 0 0 0 -9 +NPE826 NPE826 0 0 0 -9 +ORYZICASABANA6 ORYZICASABANA6 0 0 0 -9 +OS4 OS4 0 0 0 -9 +OS6 OS6 0 0 0 -9 +P5589-1-1-3-P P5589-1-1-3-P 0 0 0 -9 +PACHOLINHA PACHOLINHA 0 0 0 -9 +PADIBOENAR PADIBOENAR 0 0 0 -9 +PADIKASALLE PADIKASALLE 0 0 0 -9 +PALAWAN PALAWAN 0 0 0 -9 +PATEBLANCMAN1 PATEBLANCMAN1 0 0 0 -9 +PCT11_0_0_2_BO_1_55-1-3-1 PCT11_0_0_2_BO_1_55-1-3-1 0 0 0 -9 +PCT4_SA_4_1_1076-2-4-1-5 PCT4_SA_4_1_1076-2-4-1-5 0 0 0 -9 +PEHPINUO PEHPINUO 0 0 0 -9 +POENOETHITAM POENOETHITAM 0 0 0 -9 +PULULAPA PULULAPA 0 0 0 -9 +RATHAL RATHAL 0 0 0 -9 +REKETMAUN REKETMAUN 0 0 0 -9 +RT1031-69 RT1031-69 0 0 0 -9 +SENG SENG 0 0 0 -9 +SPEAKER SPEAKER 0 0 0 -9 +TANDUI TANDUI 0 0 0 -9 +TREMBESE TREMBESE 0 0 0 -9 +TRESMESES TRESMESES 0 0 0 -9 +TSIPALA89 TSIPALA89 0 0 0 -9 +VARYLAVA90 VARYLAVA90 0 0 0 -9 +VARYLAVADEBETAFO VARYLAVADEBETAFO 0 0 0 -9 +VARYMADINIKA3566 VARYMADINIKA3566 0 0 0 -9 +VARYMALADY VARYMALADY 0 0 0 -9 +VARYSOMOTRASIHANAKA VARYSOMOTRASIHANAKA 0 0 0 -9 +WAB56-125 WAB56-125 0 0 0 -9 +WAB56-50 WAB56-50 0 0 0 -9 +WAB706-3-4-K4-KB-1 WAB706-3-4-K4-KB-1 0 0 0 -9 +YANCAOUSSA YANCAOUSSA 0 0 0 -9 +YANGKUMRED YANGKUMRED 0 0 0 -9 +YUNLU7 YUNLU7 0 0 0 -9 +IR47686-09-01-B-1 IR47686-09-01-B-1 0 0 0 -9 +IR53236-275-1 IR53236-275-1 0 0 0 -9 +IR65261-19-1-B IR65261-19-1-B 0 0 0 -9 +IR65907-206-4-B IR65907-206-4-B 0 0 0 -9 +IR66421-105-1-1 IR66421-105-1-1 0 0 0 -9 +IR71524-44-1-1 IR71524-44-1-1 0 0 0 -9 +VIETNAM1 VIETNAM1 0 0 0 -9 +VIETNAM3 VIETNAM3 0 0 0 -9 +IR47684-05-1-B IR47684-05-1-B 0 0 0 -9 +PRIMAVERA PRIMAVERA 0 0 0 -9 +CHUAN3 CHUAN3 0 0 0 -9 +CHUAN4 CHUAN4 0 0 0 -9 +EARLYMUTANTIAC165 EARLYMUTANTIAC165 0 0 0 -9
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output Tue Apr 12 08:32:23 2016 -0400 @@ -0,0 +1,168 @@ +<Covariate> +<Trait> Q1 Q2 Q3 +GIZA171 0.586741 0.000010 0.413249 +IAC165 0.945312 0.006465 0.048224 +M202 0.999980 0.000010 0.000010 +MOROBEREKAN 0.831922 0.000010 0.168068 +62667 0.983237 0.016753 0.000010 +BAGANANASALAO 0.736051 0.263939 0.000010 +CHAPHUMA 0.801557 0.000010 0.198433 +CICIHBETON 0.999980 0.000010 0.000010 +CIRAD358 0.569210 0.000010 0.430780 +DANGREY 0.999980 0.000010 0.000010 +DAVAO 0.999980 0.000010 0.000010 +DINORADO 0.992108 0.007882 0.000010 +GOGO 0.999980 0.000010 0.000010 +GRAZI 0.844812 0.097165 0.058023 +HAWMOM 0.586615 0.000010 0.413375 +HD1-4 0.999980 0.000010 0.000010 +IR60080-46A 0.825891 0.000010 0.174099 +JIMBRUKJOLOWORO 0.999980 0.000010 0.000010 +JUMULA2 0.747177 0.163796 0.089027 +KAKANI2 0.790361 0.070580 0.139059 +KANIRANGA 0.855150 0.125292 0.019558 +KEDAYAN 0.999980 0.000010 0.000010 +KETANMENAH 0.650538 0.000010 0.349452 +KINANDANGPATONG 0.999980 0.000010 0.000010 +KUROKA 0.999980 0.000010 0.000010 +LAMBAYQUE1 0.671645 0.000010 0.328345 +LUDAN 0.709814 0.231278 0.058908 +MAINTIMOLOTSY1226 0.999980 0.000010 0.000010 +NABESHI 0.614509 0.000010 0.385481 +NEPHOAVANG 0.999980 0.000010 0.000010 +NHTA10 0.881379 0.118611 0.000010 +NHTA5 0.873563 0.000010 0.126427 +NPE253 0.712232 0.157112 0.130656 +NPE826 0.999980 0.000010 0.000010 +ORYZICASABANA6 0.999980 0.000010 0.000010 +PADIKASALLE 0.596822 0.000010 0.403168 +PALAWAN 0.538069 0.000010 0.461921 +POENOETHITAM 0.999980 0.000010 0.000010 +PULULAPA 0.629810 0.000010 0.370180 +RT1031-69 0.604237 0.000010 0.395753 +SPEAKER 0.999980 0.000010 0.000010 +YUNLU7 0.999980 0.000010 0.000010 +IR47686-09-01-B-1 0.657103 0.000010 0.342887 +VIETNAM3 0.999980 0.000010 0.000010 +IR47684-05-1-B 0.999980 0.000010 0.000010 +CHUAN4 0.999980 0.000010 0.000010 +EARLYMUTANTIAC165 0.999980 0.000010 0.000010 +CIRAD409 0.000010 0.759299 0.240691 +CIRAD488 0.000010 0.600168 0.399822 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+BAKUNGH 0.180348 0.000010 0.819642 +BENGALYVAKARINA 0.116979 0.000010 0.883011 +BICOBRANCO 0.210938 0.000010 0.789052 +BINULAWAN 0.000010 0.000010 0.999980 +CAAWA/FORTUNA6 0.082859 0.000010 0.917131 +CAIAPO 0.115889 0.000010 0.884101 +CANAROXA 0.134469 0.000010 0.865521 +CANELADEFERRO 0.000010 0.000010 0.999980 +CHALOYOE 0.000010 0.000010 0.999980 +CIRAD392 0.442360 0.000010 0.557630 +CIRAD394 0.204730 0.107281 0.687989 +CIRAD403 0.242768 0.126952 0.630280 +CNA-7_BO_1_1_33-13-6-1 0.196055 0.081135 0.722809 +CUBA65 0.000010 0.487001 0.512989 +CUIABANA 0.155072 0.000010 0.844918 +CURINCA 0.471804 0.000010 0.528186 +DAWASANRED 0.053031 0.000010 0.946959 +DOURADOAGULHA 0.085429 0.000010 0.914561 +DOURADOPRECOCE 0.000010 0.000010 0.999980 +ESPERANZA 0.000010 0.000010 0.999980 +FOHISOMOTRA 0.000010 0.359984 0.640006 +GANIGI 0.000010 0.000010 0.999980 +GEMJYAJYANAM 0.197535 0.000010 0.802455 +GOGOLEMPUK 0.220531 0.000010 0.779459 +GOGOLEMPAK 0.450796 0.000010 0.549194 +GOMPA2 0.454524 0.000010 0.545466 +GUARANI 0.000010 0.000010 0.999980 +GUNDILKUNING 0.000010 0.000010 0.999980 +IAC25 0.000010 0.000010 0.999980 +IAC47 0.000010 0.000010 0.999980 +IDSA77 0.000010 0.000010 0.999980 +INDANE 0.000010 0.000010 0.999980 +IR63372-08 0.000010 0.402550 0.597440 +IRAT104 0.000010 0.430660 0.569330 +IRAT109 0.000010 0.000010 0.999980 +IRAT112 0.155698 0.109413 0.734889 +IRAT13 0.000010 0.000010 0.999980 +IRAT144 0.000010 0.012649 0.987341 +IRAT170 0.191251 0.036820 0.771930 +IRAT177 0.000010 0.000010 0.999980 +IRAT2 0.000010 0.000010 0.999980 +IRAT212 0.000010 0.000010 0.999980 +IRAT216 0.212135 0.023321 0.764544 +IRAT257 0.000010 0.000010 0.999980 +IRAT335 0.000010 0.000010 0.999980 +IRAT362 0.000010 0.270513 0.729477 +IRAT364 0.000010 0.321994 0.677996 +IRAT366 0.000010 0.000010 0.999980 +IRAT380 0.000010 0.000010 0.999980 +JAOHAW 0.168986 0.099515 0.731499 +JUMALI 0.312901 0.000010 0.687089 +KARASUKARASURANKASU 0.304195 0.000010 0.695795 +KENDINGA5H 0.190313 0.000010 0.809677 +KETANKONIR 0.127600 0.000010 0.872390 +KETANLUMBU 0.303188 0.000010 0.696802 +KHAOKAPXANG 0.219799 0.000010 0.780191 +KOMOJAMANITRA 0.000010 0.088058 0.911932 +KU115 0.080829 0.000010 0.919161 +MAHAE 0.161806 0.000010 0.838184 +MALAGKITPIRURUTONG 0.000010 0.000010 0.999980 +MANANELATRA520 0.116010 0.000010 0.883980 +MANDRIRAVINA3512 0.000010 0.000010 0.999980 +MARAVILHA 0.000010 0.000010 0.999980 +MOLOK 0.224580 0.076683 0.698737 +OS4 0.000010 0.384119 0.615871 +OS6 0.000010 0.000010 0.999980 +P5589-1-1-3-P 0.000010 0.000010 0.999980 +PACHOLINHA 0.000010 0.382637 0.617353 +PADIBOENAR 0.000010 0.000010 0.999980 +PATEBLANCMAN1 0.062371 0.000010 0.937619 +PCT11_0_0_2_BO_1_55-1-3-1 0.145774 0.000010 0.854216 +RATHAL 0.169700 0.004321 0.825979 +REKETMAUN 0.179511 0.000010 0.820479 +SENG 0.000010 0.000010 0.999980 +TANDUI 0.000010 0.000010 0.999980 +TREMBESE 0.221145 0.000010 0.778845 +TRESMESES 0.397909 0.000010 0.602081 +TSIPALA89 0.000010 0.000010 0.999980 +VARYLAVA90 0.072332 0.000010 0.927658 +VARYLAVADEBETAFO 0.000010 0.000010 0.999980 +VARYMADINIKA3566 0.063055 0.127148 0.809797 +VARYMALADY 0.154619 0.000010 0.845371 +VARYSOMOTRASIHANAKA 0.161759 0.000010 0.838231 +WAB56-125 0.060129 0.000010 0.939861 +YANCAOUSSA 0.000010 0.139600 0.860390 +YANGKUMRED 0.134426 0.000010 0.865564 +IR53236-275-1 0.000010 0.000010 0.999980 +IR65261-19-1-B 0.102795 0.000010 0.897195 +VIETNAM1 0.000010 0.112662 0.887328 +CHUAN3 0.290550 0.026546 0.682904 +PCT4_SA_4_1_1076-2-4-1-5 0.123261 0.473604 0.403136 +IR65907-206-4-B 0.169741 0.341301 0.488957
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs.Q Tue Apr 12 08:32:23 2016 -0400 @@ -0,0 +1,342 @@ +BULUPANDAK 0.820166 0.179834 +KHAODAM 0.999990 0.000010 +NIPPONBARE_D 0.748877 0.251123 +63-104 0.999990 0.000010 +ARAGUAIA 0.999990 0.000010 +ARIAS 0.999990 0.000010 +ARROZCEBADA 0.746417 0.253583 +BABER 0.999990 0.000010 +BAKUNGH 0.767720 0.232280 +BENGALYVAKARINA 0.827800 0.172200 +BICOBRANCO 0.671502 0.328498 +BINULAWAN 0.999990 0.000010 +CAAWA/FORTUNA6 0.855007 0.144993 +CAIAPO 0.844450 0.155550 +CANAROXA 0.833462 0.166538 +CANELADEFERRO 0.997417 0.002583 +CHALOYOE 0.999990 0.000010 +CIRAD394 0.761822 0.238178 +CIRAD403 0.735955 0.264045 +CIRAD409 0.999990 0.000010 +CIRAD488 0.999990 0.000010 +CNA-7_BO_1_1_33-13-6-1 0.778845 0.221155 +COLOMBIA1 0.952970 0.047030 +CT13582-15-5-M 0.870019 0.129981 +CUBA65 0.999990 0.000010 +CUIABANA 0.780953 0.219047 +DAM 0.999990 0.000010 +DAWASANRED 0.884809 0.115191 +DOURADOAGULHA 0.838808 0.161192 +DOURADOPRECOCE 0.999990 0.000010 +ESPERANZA 0.999990 0.000010 +FOHISOMOTRA 0.983615 0.016385 +GANIGI 0.887626 0.112374 +GEMJYAJYANAM 0.712536 0.287464 +GOGOLEMPUK 0.700984 0.299016 +GUARANI 0.999990 0.000010 +GUNDILKUNING 0.999990 0.000010 +IAC25 0.999990 0.000010 +IAC47 0.999990 0.000010 +IDSA77 0.999990 0.000010 +IGUAPECATETO 0.999990 0.000010 +INDANE 0.999990 0.000010 +IR63380-16 0.999990 0.000010 +IR63372-08 0.999990 0.000010 +IR65907-188-1-B 0.965010 0.034990 +IR66421-096-2-1-1 0.939358 0.060642 +IR68704-145-1-1-B 0.778088 0.221912 +IR71525-19-1-1 0.909494 0.090506 +IRAT104 0.999990 0.000010 +IRAT109 0.999990 0.000010 +IRAT112 0.835401 0.164599 +IRAT13 0.999990 0.000010 +IRAT144 0.999990 0.000010 +IRAT170 0.787529 0.212471 +IRAT177 0.999990 0.000010 +IRAT2 0.999990 0.000010 +IRAT212 0.999990 0.000010 +IRAT216 0.726907 0.273093 +IRAT234 0.999990 0.000010 +IRAT257 0.999990 0.000010 +IRAT335 0.999990 0.000010 +IRAT362 0.970619 0.029381 +IRAT364 0.999990 0.000010 +IRAT366 0.981389 0.018611 +IRAT380 0.999990 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Apr 12 08:32:23 2016 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="admixture" version="1.23"> + <repository changeset_revision="0f7e9a05a299" name="package_admixture_1_23" owner="dereeper" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>