# HG changeset patch
# User devteam
# Date 1447090473 18000
# Node ID 59d4413e75ebb22be7aba4d43f67b10b93c23342
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
diff -r 000000000000 -r 59d4413e75eb macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Nov 09 12:34:33 2015 -0500
@@ -0,0 +1,28 @@
+
+
+
+ vcflib
+
+
+
+
+
+
+
+
+
+
+
+@misc{Garrison2015,
+ author = {Garrison, Erik},
+ year = {2015},
+ title = {vcflib},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/ekg/vcflib},
+}
+
+
+
+ is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
+
diff -r 000000000000 -r 59d4413e75eb test-data/vcfsort-test1-input.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfsort-test1-input.vcf Mon Nov 09 12:34:33 2015 -0500
@@ -0,0 +1,30 @@
+##fileformat=VCFv4.0
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##FILTER=
+##FILTER=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##ALT=
+##ALT=
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
+20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
+20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,.
+20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
+20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,.
+20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3
+20 1235237 . T . . . . GT 0/0 0|0 ./.
+19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3
+19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3
diff -r 000000000000 -r 59d4413e75eb test-data/vcfsort-test1.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfsort-test1.vcf Mon Nov 09 12:34:33 2015 -0500
@@ -0,0 +1,30 @@
+##fileformat=VCFv4.0
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##FILTER=
+##FILTER=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##ALT=
+##ALT=
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
+19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3
+19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3
+20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
+20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,.
+20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
+20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,.
+20 1234567 microsat1 G GA,GAC 50 PASS NS=3;DP=9;AA=G;AN=6;AC=3,1 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3
+20 1235237 . T . . . . GT 0/0 0|0 ./.
diff -r 000000000000 -r 59d4413e75eb vcfsort.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfsort.xml Mon Nov 09 12:34:33 2015 -0500
@@ -0,0 +1,27 @@
+
+ Sort VCF dataset by coordinate
+ (grep ^"#" "${input1}"; grep -v ^"#" "${input1}" | LC_ALL=C sort -k1,1 -k2,2n -V) > "${out_file1}"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+This tool uses native UNIX sort command to order VCF dataset in coordinate order. For technically inclined the command is::
+
+ (grep ^"#" INPUT_file ; grep -v ^"#" INPUT_file | LC_ALL=C sort -k1,1 -k2,2n -V) > OUTPUT_file
+
+.. class:: infomark
+
+The same result can be achieved with the Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order).
+
+
+