| Previous changeset 3:70bc6ced57f7 (2018-03-26) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 36e9065027cc7bf721e9d203208477ee88906c57" |
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modified:
macros.xml test-data/vcfannotategenotypes-test1.vcf vcfannotategenotypes.xml |
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| diff -r 70bc6ced57f7 -r 84959112d9a6 macros.xml --- a/macros.xml Mon Mar 26 12:20:23 2018 -0400 +++ b/macros.xml Thu Jan 23 08:04:28 2020 -0500 |
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| @@ -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> |
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| diff -r 70bc6ced57f7 -r 84959112d9a6 test-data/vcfannotategenotypes-test1.vcf --- a/test-data/vcfannotategenotypes-test1.vcf Mon Mar 26 12:20:23 2018 -0400 +++ b/test-data/vcfannotategenotypes-test1.vcf Thu Jan 23 08:04:28 2020 -0500 |
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| @@ -22,12 +22,12 @@ ##INFO=<ID=added-genotypes.has_variant,Number=0,Type=Flag,Description="True if added-genotypes has a called alternate among samples under comparison."> ##FORMAT=<ID=added-genotypes,Number=1,Type=String,Description="Genotype from added-genotypes."> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 -19 111 . A C 9.6 . added-genotypes.has_variant GT:HQ:added-genotypes 0|0:10,10:0/0 0|0:10,10:./. 0/1:3,3:0/1 -19 112 . A G 10 . added-genotypes.has_variant GT:HQ:added-genotypes 0|0:10,10:0/0 0|0:10,10:./. 0/1:3,3:0/1 -20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:48:1:51,51:0/0 1|0:48:8:51,51:./. 1/1:43:5:.,.:1/1 -20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:49:3:58,50:0/0 0|1:3:5:65,3:./. 0/0:41:3:.,.:0/0 -20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 1|2:21:6:23,27:1/2 2|1:2:0:18,2:./. 2/2:35:4:.,.:2/2 -20 1230237 . T . 47 PASS AA=T;DP=13;NS=3;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:54:.:56,60:0/0 0|0:48:4:51,51:./. 0/0:61:2:.,.:0/0 +19 111 . A C 9.6 . added-genotypes.has_variant GT:HQ:added-genotypes 0|0:10,10:0|0 0|0:10,10:./. 0/1:3,3:0/1 +19 112 . A G 10 . added-genotypes.has_variant GT:HQ:added-genotypes 0|0:10,10:0|0 0|0:10,10:./. 0/1:3,3:0/1 +20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:48:1:51,51:0|0 1|0:48:8:51,51:./. 1/1:43:5:.,.:1/1 +20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:49:3:58,50:0|0 0|1:3:5:65,3:./. 0/0:41:3:.,.:0/0 +20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 1|2:21:6:23,27:1|2 2|1:2:0:18,2:./. 2/2:35:4:.,.:2/2 +20 1230237 . T . 47 PASS AA=T;DP=13;NS=3;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:54:.:56,60:0|0 0|0:48:4:51,51:./. 0/0:61:2:.,.:0/0 20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3;added-genotypes.has_variant GT:GQ:DP:added-genotypes 0/1:.:4:0/1 0/2:17:2:./. 1/1:40:3:1/1 20 1235237 . T . 0 . added-genotypes.has_variant GT:added-genotypes 0/0:0/0 0|0:./. ./.:. -X 10 rsTest AC A,ATG 10 PASS added-genotypes.has_variant GT:added-genotypes 0:0 0/1:./. 0|2:0/2 +X 10 rsTest AC A,ATG 10 PASS added-genotypes.has_variant GT:added-genotypes 0:0 0/1:./. 0|2:0|2 |
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| diff -r 70bc6ced57f7 -r 84959112d9a6 vcfannotategenotypes.xml --- a/vcfannotategenotypes.xml Mon Mar 26 12:20:23 2018 -0400 +++ b/vcfannotategenotypes.xml Thu Jan 23 08:04:28 2020 -0500 |
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| @@ -5,7 +5,7 @@ </macros> <expand macro="requirements"/> <expand macro="stdio" /> - <command>vcfannotategenotypes "${tag_option}" "${input1}" "${input2}" > "${out_file1}"</command> + <command>vcfannotategenotypes '${tag_option}' '${input1}' '${input2}' > '${out_file1}'</command> <inputs> <param format="vcf" name="input1" type="data" label="Annotate genotypes in" help="First VCF dataset"/> <param format="vcf" name="input2" type="data" label="using genotypes from" help="Second VCF dataset"/> |