Mercurial > repos > devteam > vcf2tsv
changeset 4:285060661b45 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv commit 36e9065027cc7bf721e9d203208477ee88906c57"
| author | iuc |
|---|---|
| date | Thu, 23 Jan 2020 08:00:49 -0500 |
| parents | e92b3c0f9224 |
| children | |
| files | macros.xml test-data/vcf2tsv-test1.tab test-data/vcf2tsv-test2.tab |
| diffstat | 3 files changed, 58 insertions(+), 49 deletions(-) [+] |
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--- a/macros.xml Mon Mar 26 12:17:07 2018 -0400 +++ b/macros.xml Thu Jan 23 08:00:49 2020 -0500 @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="1.0.0_rc1">vcflib</requirement> + <requirement type="package" version="1.0.0_rc3">vcflib</requirement> <yield/> </requirements> </xml> @@ -10,10 +10,10 @@ <exit_code range="1:" level="fatal" /> </stdio> </xml> - <token name="@WRAPPER_VERSION@">1.0.0_rc1</token> - <xml name="citations"> - <citations> - <citation type="bibtex"> + <token name="@WRAPPER_VERSION@">1.0.0_rc3</token> + <xml name="citations"> + <citations> + <citation type="bibtex"> @misc{Garrison2015, author = {Garrison, Erik}, year = {2015}, @@ -22,8 +22,8 @@ journal = {GitHub repository}, url = {https://github.com/ekg/vcflib}, } - </citation> - </citations> - </xml> + </citation> + </citations> + </xml> <token name="@IS_PART_OF_VCFLIB@">is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).</token> </macros>
--- a/test-data/vcf2tsv-test1.tab Mon Mar 26 12:17:07 2018 -0400 +++ b/test-data/vcf2tsv-test1.tab Thu Jan 23 08:00:49 2020 -0500 @@ -1,28 +1,37 @@ -CHROM POS ID REF ALT QUAL FILTER AA AC AF AN DP NS DB H2 SAMPLE DP GQ GT HQ -19 111 . A C 9.6 . . . . . . . 0 0 NA00001 . . 0|0 10,10 -19 111 . A C 9.6 . . . . . . . 0 0 NA00002 . . 0|0 10,10 -19 111 . A C 9.6 . . . . . . . 0 0 NA00003 . . 0/1 3,3 -19 112 . A G 10 . . . . . . . 0 0 NA00001 . . 0|0 10,10 -19 112 . A G 10 . . . . . . . 0 0 NA00002 . . 0|0 10,10 -19 112 . A G 10 . . . . . . . 0 0 NA00003 . . 0/1 3,3 -20 14370 rs6054257 G A 29 PASS . . 0.5 . 14 3 1 1 NA00001 1 48 0|0 51,51 -20 14370 rs6054257 G A 29 PASS . . 0.5 . 14 3 1 1 NA00002 8 48 1|0 51,51 -20 14370 rs6054257 G A 29 PASS . . 0.5 . 14 3 1 1 NA00003 5 43 1/1 .,. -20 17330 . T A 3 q10 . . 0.017 . 11 3 0 0 NA00001 3 49 0|0 58,50 -20 17330 . T A 3 q10 . . 0.017 . 11 3 0 0 NA00002 5 3 0|1 65,3 -20 17330 . T A 3 q10 . . 0.017 . 11 3 0 0 NA00003 3 41 0/0 .,. -20 1110696 rs6040355 A G,T 67 PASS T . 0.333,0.667 . 10 2 1 0 NA00001 6 21 1|2 23,27 -20 1110696 rs6040355 A G,T 67 PASS T . 0.333,0.667 . 10 2 1 0 NA00002 0 2 2|1 18,2 -20 1110696 rs6040355 A G,T 67 PASS T . 0.333,0.667 . 10 2 1 0 NA00003 4 35 2/2 .,. -20 1230237 . T . 47 PASS T . . . 13 3 0 0 NA00001 . 54 0|0 56,60 -20 1230237 . T . 47 PASS T . . . 13 3 0 0 NA00002 4 48 0|0 51,51 -20 1230237 . T . 47 PASS T . . . 13 3 0 0 NA00003 2 61 0/0 .,. -20 1234567 microsat1 G GA,GAC 50 PASS G 3,1 . 6 9 3 0 0 NA00001 4 . 0/1 . -20 1234567 microsat1 G GA,GAC 50 PASS G 3,1 . 6 9 3 0 0 NA00002 2 17 0/2 . -20 1234567 microsat1 G GA,GAC 50 PASS G 3,1 . 6 9 3 0 0 NA00003 3 40 1/1 . -20 1235237 . T . 0 . . . . . . . 0 0 NA00001 . . 0/0 . -20 1235237 . T . 0 . . . . . . . 0 0 NA00002 . . 0|0 . -20 1235237 . T . 0 . . . . . . . 0 0 NA00003 . . ./. . -X 10 rsTest AC A,ATG 10 PASS . . . . . . 0 0 NA00001 . . 0 . -X 10 rsTest AC A,ATG 10 PASS . . . . . . 0 0 NA00002 . . 0/1 . -X 10 rsTest AC A,ATG 10 PASS . . . . . . 0 0 NA00003 . . 0|2 . +#CHROM POS ID REF ALT QUAL FILTER AA AC AF AN DB DP H2 NS SAMPLE DP GQ GT HQ +19 111 . A C 9.6 . . . . . . . . . NA00001 . . 0|0 10,10 +19 111 . A C 9.6 . . . . . . . . . NA00002 . . 0|0 10,10 +19 111 . A C 9.6 . . . . . . . . . NA00003 . . 0/1 3,3 +19 112 . A G 10 . . . . . . . . . NA00001 . . 0|0 10,10 +19 112 . A G 10 . . . . . . . . . NA00002 . . 0|0 10,10 +19 112 . A G 10 . . . . . . . . . NA00003 . . 0/1 3,3 +20 14370 rs6054257 G A 29 PASS . . 0.5 . . 14 . 3 NA00001 1 48 0|0 51,51 +20 14370 rs6054257 G A 29 PASS . . 0.5 . . 14 . 3 NA00002 8 48 1|0 51,51 +20 14370 rs6054257 G A 29 PASS . . 0.5 . . 14 . 3 NA00003 5 43 1/1 .,. +20 17330 . T A 3 q10 . . 0.017 . . 11 . 3 NA00001 3 49 0|0 58,50 +20 17330 . T A 3 q10 . . 0.017 . . 11 . 3 NA00002 5 3 0|1 65,3 +20 17330 . T A 3 q10 . . 0.017 . . 11 . 3 NA00003 3 41 0/0 .,. +20 1110696 rs6040355 A G 67 PASS T . 0.333,0.667 . . 10 . 2 NA00001 6 21 1|2 23,27 +20 1110696 rs6040355 A G 67 PASS T . 0.333,0.667 . . 10 . 2 NA00002 0 2 2|1 18,2 +20 1110696 rs6040355 A G 67 PASS T . 0.333,0.667 . . 10 . 2 NA00003 4 35 2/2 .,. +20 1110696 rs6040355 A T 67 PASS T . 0.333,0.667 . . 10 . 2 NA00001 6 21 1|2 23,27 +20 1110696 rs6040355 A T 67 PASS T . 0.333,0.667 . . 10 . 2 NA00002 0 2 2|1 18,2 +20 1110696 rs6040355 A T 67 PASS T . 0.333,0.667 . . 10 . 2 NA00003 4 35 2/2 .,. +20 1230237 . T . 47 PASS T . . . . 13 . 3 NA00001 . 54 0|0 56,60 +20 1230237 . T . 47 PASS T . . . . 13 . 3 NA00002 4 48 0|0 51,51 +20 1230237 . T . 47 PASS T . . . . 13 . 3 NA00003 2 61 0/0 .,. +20 1234567 microsat1 G GA 50 PASS G 3,1 . 6 . 9 . 3 NA00001 4 . 0/1 . +20 1234567 microsat1 G GA 50 PASS G 3,1 . 6 . 9 . 3 NA00002 2 17 0/2 . +20 1234567 microsat1 G GA 50 PASS G 3,1 . 6 . 9 . 3 NA00003 3 40 1/1 . +20 1234567 microsat1 G GAC 50 PASS G 3,1 . 6 . 9 . 3 NA00001 4 . 0/1 . +20 1234567 microsat1 G GAC 50 PASS G 3,1 . 6 . 9 . 3 NA00002 2 17 0/2 . +20 1234567 microsat1 G GAC 50 PASS G 3,1 . 6 . 9 . 3 NA00003 3 40 1/1 . +20 1235237 . T . 0 . . . . . . . . . NA00001 . . 0/0 . +20 1235237 . T . 0 . . . . . . . . . NA00002 . . 0|0 . +20 1235237 . T . 0 . . . . . . . . . NA00003 . . ./. . +X 10 rsTest AC A 10 PASS . . . . . . . . NA00001 . . 0 . +X 10 rsTest AC A 10 PASS . . . . . . . . NA00002 . . 0/1 . +X 10 rsTest AC A 10 PASS . . . . . . . . NA00003 . . 0|2 . +X 10 rsTest AC ATG 10 PASS . . . . . . . . NA00001 . . 0 . +X 10 rsTest AC ATG 10 PASS . . . . . . . . NA00002 . . 0/1 . +X 10 rsTest AC ATG 10 PASS . . . . . . . . NA00003 . . 0|2 .
--- a/test-data/vcf2tsv-test2.tab Mon Mar 26 12:17:07 2018 -0400 +++ b/test-data/vcf2tsv-test2.tab Thu Jan 23 08:00:49 2020 -0500 @@ -1,13 +1,13 @@ -CHROM POS ID REF ALT QUAL FILTER AA AC AF AN DP NS DB H2 -19 111 . A C 9.6 . . . . . . . 0 0 -19 112 . A G 10 . . . . . . . 0 0 -20 14370 rs6054257 G A 29 PASS . . 0.5 . 14 3 1 1 -20 17330 . T A 3 q10 . . 0.017 . 11 3 0 0 -20 1110696 rs6040355 A G 67 PASS T . 0.333 . 10 2 1 0 -20 1110696 rs6040355 A T 67 PASS T . 0.667 . 10 2 1 0 -20 1230237 . T . 47 PASS T . . . 13 3 0 0 -20 1234567 microsat1 G GA 50 PASS G 3 . 6 9 3 0 0 -20 1234567 microsat1 G GAC 50 PASS G 1 . 6 9 3 0 0 -20 1235237 . T . 0 . . . . . . . 0 0 -X 10 rsTest AC A 10 PASS . . . . . . 0 0 -X 10 rsTest AC ATG 10 PASS . . . . . . 0 0 +#CHROM POS ID REF ALT QUAL FILTER AA AC AF AN DB DP H2 NS +19 111 . A C 9.6 . . . . . . . . . +19 112 . A G 10 . . . . . . . . . +20 14370 rs6054257 G A 29 PASS . . 0.5 . . 14 . 3 +20 17330 . T A 3 q10 . . 0.017 . . 11 . 3 +20 1110696 rs6040355 A G 67 PASS T . 0.333,0.667 . . 10 . 2 +20 1110696 rs6040355 A T 67 PASS T . 0.333,0.667 . . 10 . 2 +20 1230237 . T . 47 PASS T . . . . 13 . 3 +20 1234567 microsat1 G GA 50 PASS G 3,1 . 6 . 9 . 3 +20 1234567 microsat1 G GAC 50 PASS G 3,1 . 6 . 9 . 3 +20 1235237 . T . 0 . . . . . . . . . +X 10 rsTest AC A 10 PASS . . . . . . . . +X 10 rsTest AC ATG 10 PASS . . . . . . . .