# HG changeset patch # User iuc # Date 1650305096 0 # Node ID 1932808c6fab5168e4c17b9eebd99c40d0f2b159 # Parent ec2bc87ebd7bcdc9fdcac70d5bf81a0175517806 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 1c50106137c5b3260f18864ac9084056fa91ec80" diff -r ec2bc87ebd7b -r 1932808c6fab king.xml --- a/king.xml Tue Nov 16 20:14:31 2021 +0000 +++ b/king.xml Mon Apr 18 18:04:56 2022 +0000 @@ -2,82 +2,266 @@ Kinship-based INference for GWAS - 2.2.4 + 2.2.7 0 king - r-kinship2 - r-igraph + r-kinship2 + r-igraph + r-e1071 king | head -1 | cut -d' ' -f 2 '$kingoutlog' ]]> - - - + - - - - - - - - - - - - - +
+ + +
+ +
+ + + + +
+
+ + +
+
+ + + +
+
+ + +
+
+ + +
+
+ + + +
+
+ +
+
+ +
+
+ + +
+
+ + +
+
+ + + + +
+
+ + + +
+
+ + + +
+ use_log == True - + + + + use_log == True - + + - + opt_par["rplot"] or opt_par["pngplot"] + + - + - - - +
+ + +
+
+ +
@@ -88,12 +272,18 @@ - + - - - - +
+ + +
+
+ +
+
+ +
@@ -105,13 +295,21 @@ - + - - - - - +
+ + +
+
+ +
+
+ +
+
+ +
@@ -125,11 +323,15 @@ - + - - - +
+ + +
+
+ +
@@ -139,11 +341,15 @@ - + - - - +
+ + +
+
+ +
@@ -153,12 +359,18 @@ - + - - - - +
+ + +
+
+ +
+
+ +
@@ -171,11 +383,15 @@ - + - - - +
+ + +
+
+ +
@@ -186,13 +402,21 @@ - + - - - - - +
+ + +
+
+ +
+
+ +
+
+ +
@@ -204,11 +428,15 @@ - + - - - +
+ + +
+
+ +
@@ -222,11 +450,15 @@ - + - - - +
+ + +
+
+ +
@@ -237,11 +469,15 @@ - + - - - +
+ + +
+
+ +
@@ -252,12 +488,18 @@ - + - - - - +
+ + +
+
+ +
+
+ +
@@ -268,11 +510,15 @@ - + - - - +
+ + +
+
+ +
@@ -283,12 +529,18 @@ - + - - - - +
+ + +
+
+ +
+
+ +
@@ -299,11 +551,15 @@ - + - - - +
+ + +
+
+ +
@@ -313,12 +569,126 @@ + + +
+ + +
+
+ + + + +
+ + + + + + + + + + + + + + + + + +
+ + +
+
+ +
+ + + + + + + + + +
+ + +
+
+ +
+
+ +
+
+ + +
+ + + + + + + + + + + + + + + + + + + + + +
+ + +
+
+ +
+
+ +
+
+ + +
+ + + + + + + + + + + + + + + + + + `_ is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) - or a sequencing project. Applications of KING include family relationship inference and pedigree error checking, - quality control, population substructure identification, forensics, gene mapping, etc. + `KING `_ is a toolset that makes use of + high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a + sequencing project. Applications of KING include family relationship inference and + pedigree error checking, quality control, population substructure identification, + forensics, gene mapping, etc. ]]> @@ -326,3 +696,4 @@ 10.1093/bioinformatics/btq559 + diff -r ec2bc87ebd7b -r 1932808c6fab test-data/king_pcplot.png Binary file test-data/king_pcplot.png has changed diff -r ec2bc87ebd7b -r 1932808c6fab test-data/subset_bed.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset_bed.sh Mon Apr 18 18:04:56 2022 +0000 @@ -0,0 +1,20 @@ +binary_file=ex.bed +target_markers=6000 +target_cols=$(( 6 + ( $target_markers * 2 ))) + +dec_prefix=out +subs_prefix=sub +new_prefix="new."${target_markers} + +##conda activate plink +## Extract binary file into new map, ped, and fam files +plink --bfile $(basename $binary_file .bed) --recode --out ${dec_prefix} + +## Subset ped and map +cat ${dec_prefix}.ped | cut -d' ' -f 1-${target_cols} > ${subs_prefix}.ped +head ${dec_prefix}.map -n ${target_markers} > ${subs_prefix}.map + +## Recode into new +plink --file ${subs_prefix} --out ${new_prefix} +echo ${new_prefix}* +##conda deactivate diff -r ec2bc87ebd7b -r 1932808c6fab test-data/test.model --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.model Mon Apr 18 18:04:56 2022 +0000 @@ -0,0 +1,9 @@ +SNP EA AF WT CHR POS OA +rs326468 A 0.131 1.702 6 32626272 C +rs6596679 G 0.095 1.801 6 32591213 A +rs1500238 T 0.076 1.367 6 32605884 C +rs664978 T 0.345 0.839 6 32583299 C +rs1161240 C 0.216 1.079 6 32450613 A +rs2602970 T 0.265 0.403 11 2182224 A +rs1161312 C 0.459 0.295 17 38066240 T +