| Previous changeset 3:428b93a3acb4 (2024-12-14) Next changeset 5:8e75b2d61784 (2025-03-01) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71 |
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added:
test-data/sample.cnv.bed test-data/sample.cnv.cdt test-data/sample.cnv.input test-data/sample.cnv.jtv test-data/sample.cnv.seg test-data/sample.cnv.tsv test-data/sample.cnv.txt test-data/sample.cnv.vcf |
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| diff -r 428b93a3acb4 -r d14cfbdd41f0 test-data/sample.cnv.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample.cnv.bed Mon Jan 20 16:43:39 2025 +0000 |
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| @@ -0,0 +1,1 @@ +chrM 848 16023 SampleID 1 |
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| diff -r 428b93a3acb4 -r d14cfbdd41f0 test-data/sample.cnv.cdt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample.cnv.cdt Mon Jan 20 16:43:39 2025 +0000 |
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| @@ -0,0 +1,57 @@ +GID CLID NAME GWEIGHT sample +AID ARRY000X +EWEIGHT 1 +GENE0X IMAGE:0 chrM:848-1121:- 1 -0.545691 +GENE1X IMAGE:1 chrM:1394-1667:- 1 0.488494 +GENE2X IMAGE:2 chrM:1667-1940:- 1 0.0200539 +GENE3X IMAGE:3 chrM:2212-2485:- 1 -0.234816 +GENE4X IMAGE:4 chrM:2485-2758:- 1 0.153636 +GENE5X IMAGE:5 chrM:2758-3031:- 1 -1.35597 +GENE6X IMAGE:6 chrM:3031-3304:- 1 0.385198 +GENE7X IMAGE:7 chrM:3306-3579:- 1 -1.37983 +GENE8X IMAGE:8 chrM:3579-3853:- 1 0.471839 +GENE9X IMAGE:9 chrM:3853-4126:- 1 0.444955 +GENE10X IMAGE:10 chrM:4126-4400:- 1 0.465611 +GENE11X IMAGE:11 chrM:4401-4695:- 1 -0.583114 +GENE12X IMAGE:12 chrM:4695-4990:- 1 1.13235 +GENE13X IMAGE:13 chrM:4990-5284:- 1 0.209867 +GENE14X IMAGE:14 chrM:5284-5579:- 1 1.18493 +GENE15X IMAGE:15 chrM:5586-5655:- 1 -21.0389 +GENE16X IMAGE:16 chrM:5656-5729:- 1 -19.8096 +GENE17X IMAGE:17 chrM:5760-5891:- 1 0.0 +GENE18X IMAGE:18 chrM:5903-6171:- 1 -0.0283011 +GENE19X IMAGE:19 chrM:6171-6440:- 1 -0.212606 +GENE20X IMAGE:20 chrM:6440-6708:- 1 -0.38297 +GENE21X IMAGE:21 chrM:6708-6977:- 1 -0.317296 +GENE22X IMAGE:22 chrM:6977-7245:- 1 -0.127011 +GENE23X IMAGE:23 chrM:7245-7514:- 1 0.72831 +GENE24X IMAGE:24 chrM:7517-7767:- 1 0.680162 +GENE25X IMAGE:25 chrM:7767-8018:- 1 -0.510836 +GENE26X IMAGE:26 chrM:8018-8269:- 1 -0.663743 +GENE27X IMAGE:27 chrM:8365-8630:- 1 0.28099 +GENE28X IMAGE:28 chrM:8630-8896:- 1 -0.154606 +GENE29X IMAGE:29 chrM:8896-9162:- 1 0.147562 +GENE30X IMAGE:30 chrM:9162-9427:- 1 0.937798 +GENE31X IMAGE:31 chrM:9693-9959:- 1 0.459741 +GENE32X IMAGE:32 chrM:9959-10224:- 1 -8.75948 +GENE33X IMAGE:33 chrM:10224-10490:- 1 0.509209 +GENE34X IMAGE:34 chrM:10490-10756:- 1 0.0655732 +GENE35X IMAGE:35 chrM:10756-11022:- 1 0.238204 +GENE36X IMAGE:36 chrM:11022-11287:- 1 1.20043 +GENE37X IMAGE:37 chrM:11287-11553:- 1 0.224804 +GENE38X IMAGE:38 chrM:11553-11819:- 1 -1.50066 +GENE39X IMAGE:39 chrM:11819-12084:- 1 0.0920864 +GENE40X IMAGE:40 chrM:12084-12350:- 1 -1.15941 +GENE41X IMAGE:41 chrM:12350-12616:- 1 -1.25242 +GENE42X IMAGE:42 chrM:12616-12882:- 1 -0.187246 +GENE43X IMAGE:43 chrM:12882-13147:- 1 0.419127 +GENE44X IMAGE:44 chrM:13147-13413:- 1 -0.730007 +GENE45X IMAGE:45 chrM:13413-13679:- 1 -0.0213761 +GENE46X IMAGE:46 chrM:13944-14210:- 1 -0.337011 +GENE47X IMAGE:47 chrM:14210-14476:- 1 -0.0427224 +GENE48X IMAGE:48 chrM:14746-14987:- 1 0.722701 +GENE49X IMAGE:49 chrM:14987-15228:- 1 -0.105067 +GENE50X IMAGE:50 chrM:15228-15470:- 1 -0.96567 +GENE51X IMAGE:51 chrM:15470-15711:- 1 0.576278 +GENE52X IMAGE:52 chrM:15711-15953:- 1 -1.38778 +GENE53X IMAGE:53 chrM:15955-16023:- 1 -21.1972 |
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| diff -r 428b93a3acb4 -r d14cfbdd41f0 test-data/sample.cnv.input --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample.cnv.input Mon Jan 20 16:43:39 2025 +0000 |
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| @@ -0,0 +1,2 @@ +#ID chrm start end tumorCount normalCount +start_1_848:end_1_16023 1 848 16023 14716 39185 |
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| diff -r 428b93a3acb4 -r d14cfbdd41f0 test-data/sample.cnv.jtv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample.cnv.jtv Mon Jan 20 16:43:39 2025 +0000 |
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| @@ -0,0 +1,55 @@ +CloneID Name sample +IMAGE: chrM:848-1121:- -0.545691 +IMAGE: chrM:1394-1667:- 0.488494 +IMAGE: chrM:1667-1940:- 0.0200539 +IMAGE: chrM:2212-2485:- -0.234816 +IMAGE: chrM:2485-2758:- 0.153636 +IMAGE: chrM:2758-3031:- -1.35597 +IMAGE: chrM:3031-3304:- 0.385198 +IMAGE: chrM:3306-3579:- -1.37983 +IMAGE: chrM:3579-3853:- 0.471839 +IMAGE: chrM:3853-4126:- 0.444955 +IMAGE: chrM:4126-4400:- 0.465611 +IMAGE: chrM:4401-4695:- -0.583114 +IMAGE: chrM:4695-4990:- 1.13235 +IMAGE: chrM:4990-5284:- 0.209867 +IMAGE: chrM:5284-5579:- 1.18493 +IMAGE: chrM:5586-5655:- -21.0389 +IMAGE: chrM:5656-5729:- -19.8096 +IMAGE: chrM:5760-5891:- 0.0 +IMAGE: chrM:5903-6171:- -0.0283011 +IMAGE: chrM:6171-6440:- -0.212606 +IMAGE: chrM:6440-6708:- -0.38297 +IMAGE: chrM:6708-6977:- -0.317296 +IMAGE: chrM:6977-7245:- -0.127011 +IMAGE: chrM:7245-7514:- 0.72831 +IMAGE: chrM:7517-7767:- 0.680162 +IMAGE: chrM:7767-8018:- -0.510836 +IMAGE: chrM:8018-8269:- -0.663743 +IMAGE: chrM:8365-8630:- 0.28099 +IMAGE: chrM:8630-8896:- -0.154606 +IMAGE: chrM:8896-9162:- 0.147562 +IMAGE: chrM:9162-9427:- 0.937798 +IMAGE: chrM:9693-9959:- 0.459741 +IMAGE: chrM:9959-10224:- -8.75948 +IMAGE: chrM:10224-10490:- 0.509209 +IMAGE: chrM:10490-10756:- 0.0655732 +IMAGE: chrM:10756-11022:- 0.238204 +IMAGE: chrM:11022-11287:- 1.20043 +IMAGE: chrM:11287-11553:- 0.224804 +IMAGE: chrM:11553-11819:- -1.50066 +IMAGE: chrM:11819-12084:- 0.0920864 +IMAGE: chrM:12084-12350:- -1.15941 +IMAGE: chrM:12350-12616:- -1.25242 +IMAGE: chrM:12616-12882:- -0.187246 +IMAGE: chrM:12882-13147:- 0.419127 +IMAGE: chrM:13147-13413:- -0.730007 +IMAGE: chrM:13413-13679:- -0.0213761 +IMAGE: chrM:13944-14210:- -0.337011 +IMAGE: chrM:14210-14476:- -0.0427224 +IMAGE: chrM:14746-14987:- 0.722701 +IMAGE: chrM:14987-15228:- -0.105067 +IMAGE: chrM:15228-15470:- -0.96567 +IMAGE: chrM:15470-15711:- 0.576278 +IMAGE: chrM:15711-15953:- -1.38778 +IMAGE: chrM:15955-16023:- -21.1972 |
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| diff -r 428b93a3acb4 -r d14cfbdd41f0 test-data/sample.cnv.seg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample.cnv.seg Mon Jan 20 16:43:39 2025 +0000 |
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| @@ -0,0 +1,2 @@ +ID chrom loc.start loc.end num.mark seg.mean +sample chrM 849 16023 54 -1.39012 |
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| diff -r 428b93a3acb4 -r d14cfbdd41f0 test-data/sample.cnv.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample.cnv.tsv Mon Jan 20 16:43:39 2025 +0000 |
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| @@ -0,0 +1,55 @@ +chromosome start end gene log2 probe +chrM 848 1121 - -0.545691 chrM:849-1121 +chrM 1394 1667 - 0.488494 chrM:1395-1667 +chrM 1667 1940 - 0.0200539 chrM:1668-1940 +chrM 2212 2485 - -0.234816 chrM:2213-2485 +chrM 2485 2758 - 0.153636 chrM:2486-2758 +chrM 2758 3031 - -1.35597 chrM:2759-3031 +chrM 3031 3304 - 0.385198 chrM:3032-3304 +chrM 3306 3579 - -1.37983 chrM:3307-3579 +chrM 3579 3853 - 0.471839 chrM:3580-3853 +chrM 3853 4126 - 0.444955 chrM:3854-4126 +chrM 4126 4400 - 0.465611 chrM:4127-4400 +chrM 4401 4695 - -0.583114 chrM:4402-4695 +chrM 4695 4990 - 1.13235 chrM:4696-4990 +chrM 4990 5284 - 0.209867 chrM:4991-5284 +chrM 5284 5579 - 1.18493 chrM:5285-5579 +chrM 5586 5655 - -21.0389 chrM:5587-5655 +chrM 5656 5729 - -19.8096 chrM:5657-5729 +chrM 5760 5891 - 0 chrM:5761-5891 +chrM 5903 6171 - -0.0283011 chrM:5904-6171 +chrM 6171 6440 - -0.212606 chrM:6172-6440 +chrM 6440 6708 - -0.38297 chrM:6441-6708 +chrM 6708 6977 - -0.317296 chrM:6709-6977 +chrM 6977 7245 - -0.127011 chrM:6978-7245 +chrM 7245 7514 - 0.72831 chrM:7246-7514 +chrM 7517 7767 - 0.680162 chrM:7518-7767 +chrM 7767 8018 - -0.510836 chrM:7768-8018 +chrM 8018 8269 - -0.663743 chrM:8019-8269 +chrM 8365 8630 - 0.28099 chrM:8366-8630 +chrM 8630 8896 - -0.154606 chrM:8631-8896 +chrM 8896 9162 - 0.147562 chrM:8897-9162 +chrM 9162 9427 - 0.937798 chrM:9163-9427 +chrM 9693 9959 - 0.459741 chrM:9694-9959 +chrM 9959 10224 - -8.75948 chrM:9960-10224 +chrM 10224 10490 - 0.509209 chrM:10225-10490 +chrM 10490 10756 - 0.0655732 chrM:10491-10756 +chrM 10756 11022 - 0.238204 chrM:10757-11022 +chrM 11022 11287 - 1.20043 chrM:11023-11287 +chrM 11287 11553 - 0.224804 chrM:11288-11553 +chrM 11553 11819 - -1.50066 chrM:11554-11819 +chrM 11819 12084 - 0.0920864 chrM:11820-12084 +chrM 12084 12350 - -1.15941 chrM:12085-12350 +chrM 12350 12616 - -1.25242 chrM:12351-12616 +chrM 12616 12882 - -0.187246 chrM:12617-12882 +chrM 12882 13147 - 0.419127 chrM:12883-13147 +chrM 13147 13413 - -0.730007 chrM:13148-13413 +chrM 13413 13679 - -0.0213761 chrM:13414-13679 +chrM 13944 14210 - -0.337011 chrM:13945-14210 +chrM 14210 14476 - -0.0427224 chrM:14211-14476 +chrM 14746 14987 - 0.722701 chrM:14747-14987 +chrM 14987 15228 - -0.105067 chrM:14988-15228 +chrM 15228 15470 - -0.96567 chrM:15229-15470 +chrM 15470 15711 - 0.576278 chrM:15471-15711 +chrM 15711 15953 - -1.38778 chrM:15712-15953 +chrM 15955 16023 - -21.1972 chrM:15956-16023 |
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| diff -r 428b93a3acb4 -r d14cfbdd41f0 test-data/sample.cnv.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample.cnv.txt Mon Jan 20 16:43:39 2025 +0000 |
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| @@ -0,0 +1,55 @@ +Chromosome Position Position Log R Ratio B-Allele Frequency +chrM 848 1121 -0.545691 0 +chrM 1394 1667 0.488494 +chrM 1667 1940 0.0200539 +chrM 2212 2485 -0.234816 +chrM 2485 2758 0.153636 +chrM 2758 3031 -1.35597 +chrM 3031 3304 0.385198 +chrM 3306 3579 -1.37983 +chrM 3579 3853 0.471839 +chrM 3853 4126 0.444955 +chrM 4126 4400 0.465611 +chrM 4401 4695 -0.583114 +chrM 4695 4990 1.13235 +chrM 4990 5284 0.209867 +chrM 5284 5579 1.18493 +chrM 5586 5655 -21.0389 +chrM 5656 5729 -19.8096 +chrM 5760 5891 0 +chrM 5903 6171 -0.0283011 +chrM 6171 6440 -0.212606 +chrM 6440 6708 -0.38297 +chrM 6708 6977 -0.317296 +chrM 6977 7245 -0.127011 +chrM 7245 7514 0.72831 +chrM 7517 7767 0.680162 +chrM 7767 8018 -0.510836 +chrM 8018 8269 -0.663743 +chrM 8365 8630 0.28099 +chrM 8630 8896 -0.154606 +chrM 8896 9162 0.147562 +chrM 9162 9427 0.937798 +chrM 9693 9959 0.459741 +chrM 9959 10224 -8.75948 +chrM 10224 10490 0.509209 +chrM 10490 10756 0.0655732 +chrM 10756 11022 0.238204 +chrM 11022 11287 1.20043 +chrM 11287 11553 0.224804 +chrM 11553 11819 -1.50066 +chrM 11819 12084 0.0920864 +chrM 12084 12350 -1.15941 +chrM 12350 12616 -1.25242 +chrM 12616 12882 -0.187246 +chrM 12882 13147 0.419127 +chrM 13147 13413 -0.730007 +chrM 13413 13679 -0.0213761 +chrM 13944 14210 -0.337011 +chrM 14210 14476 -0.0427224 +chrM 14746 14987 0.722701 +chrM 14987 15228 -0.105067 +chrM 15228 15470 -0.96567 +chrM 15470 15711 0.576278 +chrM 15711 15953 -1.38778 +chrM 15955 16023 -21.1972 |
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| diff -r 428b93a3acb4 -r d14cfbdd41f0 test-data/sample.cnv.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample.cnv.vcf Mon Jan 20 16:43:39 2025 +0000 |
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| @@ -0,0 +1,21 @@ +##fileformat=VCFv4.2 +##fileDate=20250120 +##source=CNVkit v0.9.11 +##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> +##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> +##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> +##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> +##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles"> +##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> +##INFO=<ID=FOLD_CHANGE,Number=1,Type=Float,Description="Fold change"> +##INFO=<ID=FOLD_CHANGE_LOG,Number=1,Type=Float,Description="Log fold change"> +##INFO=<ID=PROBES,Number=1,Type=Integer,Description="Number of probes in CNV"> +##ALT=<ID=DEL,Description="Deletion"> +##ALT=<ID=DUP,Description="Duplication"> +##ALT=<ID=CNV,Description="Copy number variable region"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype quality"> +##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events"> +##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleID +chrM 848 . N <DEL> . . IMPRECISE;SVTYPE=DEL;END=16023;SVLEN=-15175;FOLD_CHANGE=0.38153306589201086;FOLD_CHANGE_LOG=-1.39012;PROBES=54 GT:GQ 0/1:54 |