| Previous changeset 2:98fe794d2ec0 (2022-09-04) Next changeset 4:63b68fe4af85 (2024-03-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1 |
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modified:
deepvariant.xml macros.xml test-data/output.g.vcf test-data/output.vcf test-data/report.html |
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| diff -r 98fe794d2ec0 -r 918c8b94c8d8 deepvariant.xml --- a/deepvariant.xml Sun Sep 04 07:54:30 2022 +0000 +++ b/deepvariant.xml Mon Apr 10 11:11:16 2023 +0000 |
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| @@ -62,6 +62,7 @@ <option value="WES">WES: Illumina whole exome sequencing</option> <option value="PACBIO">PacBio HiFi</option> <option value="HYBRID_PACBIO_ILLUMINA">Hybrid PacBio HiFi-Illumina</option> + <option value="ONT_R104">ONT R10.4 simplex and duplex data</option> </param> <conditional name="regions_conditional"> <param name="regions_option" type="select" label="Select specific regions to process" help="Restrict the analysis to specific regions. A space-separated list of chromosome regions to process. Individual elements can be region literals, such as chr20:10-20 or paths to BED files."> @@ -110,12 +111,12 @@ <output name="vcf_file" file="output.vcf" ftype="vcf"> <assert_contents> <has_text text="##fileformat=VCFv4.2"/> - <has_size value="2473"/> + <has_size value="2478" delta="10"/> </assert_contents> </output> <output name="html_report" file="report.html" ftype="html"> <assert_contents> - <has_size value="19287" delta="100"/> + <has_size value="23176" delta="100"/> </assert_contents> </output> </test> @@ -134,12 +135,12 @@ <output name="vcf_file" ftype="vcf"> <assert_contents> <has_text text="##fileformat=VCFv4.2"/> - <has_size value="1842"/> + <has_size value="1843" delta="10"/> </assert_contents> </output> <output name="html_report" ftype="html"> <assert_contents> - <has_size value="14880" delta="100"/> + <has_size value="18894" delta="100"/> </assert_contents> </output> </test> @@ -158,12 +159,12 @@ <output name="vcf_file" ftype="vcf"> <assert_contents> <has_text text="##fileformat=VCFv4.2"/> - <has_size value="1842"/> + <has_size value="1843" delta="10"/> </assert_contents> </output> <output name="html_report" ftype="html"> <assert_contents> - <has_size value="14880" delta="100"/> + <has_size value="18894" delta="100"/> </assert_contents> </output> </test> @@ -183,18 +184,18 @@ <output name="vcf_file" ftype="vcf"> <assert_contents> <has_text text="##fileformat=VCFv4.2"/> - <has_size value="1842"/> + <has_size value="1843" delta="10"/> </assert_contents> </output> <output name="gvcf_file" file="output.g.vcf" ftype="vcf"> <assert_contents> <has_text text="##fileformat=VCFv4.2"/> - <has_size value="3191"/> + <has_size value="3192" delta="10" /> </assert_contents> </output> <output name="html_report" ftype="html"> <assert_contents> - <has_size value="14880" delta="100"/> + <has_size value="18894" delta="100"/> </assert_contents> </output> </test> @@ -212,12 +213,12 @@ <output name="vcf_file" ftype="vcf"> <assert_contents> <has_text text="##fileformat=VCFv4.2"/> - <has_size value="2473"/> + <has_size value="2478"/> </assert_contents> </output> <output name="html_report" ftype="html"> <assert_contents> - <has_size value="19287" delta="100"/> + <has_size value="23176" delta="100"/> </assert_contents> </output> </test> @@ -235,12 +236,12 @@ <output name="vcf_file" ftype="vcf"> <assert_contents> <has_text text="##fileformat=VCFv4.2"/> - <has_size value="2473"/> + <has_size value="2478"/> </assert_contents> </output> <output name="html_report" ftype="html"> <assert_contents> - <has_size value="19287" delta="100"/> + <has_size value="23176" delta="100"/> </assert_contents> </output> </test> |
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| diff -r 98fe794d2ec0 -r 918c8b94c8d8 macros.xml --- a/macros.xml Sun Sep 04 07:54:30 2022 +0000 +++ b/macros.xml Mon Apr 10 11:11:16 2023 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.4.0</token> + <token name="@TOOL_VERSION@">1.5.0</token> <token name="@SUFFIX_VERSION@">0</token> <xml name="edam_ontology"> <edam_topics> |
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| diff -r 98fe794d2ec0 -r 918c8b94c8d8 test-data/output.g.vcf --- a/test-data/output.g.vcf Sun Sep 04 07:54:30 2022 +0000 +++ b/test-data/output.g.vcf Mon Apr 10 11:11:16 2023 +0000 |
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| @@ -12,7 +12,7 @@ ##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions."> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer"> ##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer."> -##DeepVariant_version=1.4.0 +##DeepVariant_version=1.5.0 ##contig=<ID=K03455,length=9719> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 K03455 1 . T <*> 0 . END=1000 GT:GQ:MIN_DP:PL 0/0:1:0:0,0,0 @@ -20,12 +20,12 @@ K03455 2001 . T <*> 0 . END=2597 GT:GQ:MIN_DP:PL 0/0:1:0:0,0,0 K03455 2598 . G <*> 0 . END=2598 GT:GQ:MIN_DP:PL ./.:0:2:59,6,0 K03455 2599 . A <*> 0 . END=2603 GT:GQ:MIN_DP:PL 0/0:6:2:0,6,59 -K03455 2604 . CCA C,<*> 7.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:7:2:0,2,0:1,0:6,16,0,990,990,990 +K03455 2604 . CCA C,<*> 3.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:3:2:0,2,0:1,0:0,9,0,990,990,990 K03455 2607 . A <*> 0 . END=2607 GT:GQ:MIN_DP:PL 0/0:6:2:0,6,59 -K03455 2608 . A T,<*> 7.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:7:2:0,2,0:1,0:6,15,0,990,990,990 -K03455 2609 . A T,<*> 6.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:6:2:0,2,0:1,0:5,17,0,990,990,990 +K03455 2608 . A T,<*> 6.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:5:2:0,2,0:1,0:4,9,0,990,990,990 +K03455 2609 . A T,<*> 5.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:4:2:0,2,0:1,0:3,9,0,990,990,990 K03455 2610 . G <*> 0 . END=2612 GT:GQ:MIN_DP:PL 0/0:6:2:0,6,59 -K03455 2613 . A T,<*> 3.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:3:2:0,2,0:1,0:0,8,0,990,990,990 +K03455 2613 . A T,<*> 0.9 RefCall . GT:GQ:DP:AD:VAF:PL ./.:7:2:0,2,0:1,0:0,10,8,990,990,990 K03455 2614 . A <*> 0 . END=2614 GT:GQ:MIN_DP:PL 0/0:6:2:0,6,59 K03455 2615 . A <*> 0 . END=2615 GT:GQ:MIN_DP:PL 0/0:15:5:0,15,149 K03455 2616 . C <*> 0 . END=2616 GT:GQ:MIN_DP:PL ./.:0:7:8,0,158 @@ -34,10 +34,10 @@ K03455 2619 . T <*> 0 . END=2619 GT:GQ:MIN_DP:PL 0/0:21:7:0,21,209 K03455 2620 . G <*> 0 . END=2620 GT:GQ:MIN_DP:PL 0/0:39:13:0,39,389 K03455 2621 . G <*> 0 . END=2651 GT:GQ:MIN_DP:PL 0/0:50:49:0,147,1469 -K03455 2652 . G A,<*> 23.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:23:201:0,201,0:1,0:23,36,0,990,990,990 +K03455 2652 . G A,<*> 27.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:27:201:0,201,0:1,0:27,34,0,990,990,990 K03455 2653 . T <*> 0 . END=2659 GT:GQ:MIN_DP:PL 0/0:50:201:0,300,2999 -K03455 2660 . T C,<*> 21.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:21:213:0,213,0:1,0:21,30,0,990,990,990 +K03455 2660 . T C,<*> 30.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:29:213:0,213,0:1,0:30,35,0,990,990,990 K03455 2661 . T <*> 0 . END=2663 GT:GQ:MIN_DP:PL 0/0:50:213:0,300,2999 -K03455 2664 . A G,<*> 21.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:21:238:0,238,0:1,0:21,33,0,990,990,990 +K03455 2664 . A G,<*> 24.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:24:238:0,238,0:1,0:24,32,0,990,990,990 K03455 2665 . C <*> 0 . END=2668 GT:GQ:MIN_DP:PL 0/0:50:240:0,300,2999 -K03455 2669 . G A,<*> 15.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:16:250:0,250,0:1,0:15,32,0,990,990,990 +K03455 2669 . G A,<*> 30.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:29:250:0,250,0:1,0:30,35,0,990,990,990 |
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| diff -r 98fe794d2ec0 -r 918c8b94c8d8 test-data/output.vcf --- a/test-data/output.vcf Sun Sep 04 07:54:30 2022 +0000 +++ b/test-data/output.vcf Mon Apr 10 11:11:16 2023 +0000 |
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| @@ -12,21 +12,21 @@ ##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions."> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer"> ##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer."> -##DeepVariant_version=1.4.0 +##DeepVariant_version=1.5.0 ##contig=<ID=K03455,length=9719> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 -K03455 2652 . G A 24.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:24:201:0,200:0.995025:24,35,0 -K03455 2660 . T C 21.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:21:213:0,213:1:21,30,0 -K03455 2664 . A G 20.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:21:238:0,238:1:20,33,0 -K03455 2669 . G A 16.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:16:258:0,250:0.968992:16,33,0 -K03455 2720 . T C 34.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:35:384:0,380:0.989583:34,49,0 -K03455 2797 . G A 38.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:37:669:0,666:0.995516:38,43,0 -K03455 2848 . T TA 39.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:36:820:85,704:0.858537:39,39,0 -K03455 2874 . C T 34.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:34:777:1,756:0.972973:34,46,0 -K03455 2882 . G T 34.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:34:737:9,721:0.97829:34,47,0 -K03455 2894 . T C 29.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:29:728:1,717:0.98489:29,51,0 -K03455 2906 . C T 16 PASS . GT:GQ:DP:AD:VAF:PL 1/1:16:653:2,650:0.995406:15,33,0 -K03455 2913 . G A 21.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:22:639:1,638:0.998435:21,40,0 -K03455 2987 . C T 4.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:4:235:0,234:0.995745:1,21,0 -K03455 3020 . A G 13.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:13:100:0,100:1:13,20,0 -K03455 3042 . A C 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:32:12:9,3:0.25:0,36,33 +K03455 2652 . G A 27.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:27:201:0,200:0.995025:27,33,0 +K03455 2660 . T C 30.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:29:213:0,213:1:30,34,0 +K03455 2664 . A G 24.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:24:238:0,238:1:24,32,0 +K03455 2669 . G A 29.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:29:258:0,250:0.968992:29,36,0 +K03455 2720 . T C 42.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:37:384:0,380:0.989583:42,38,0 +K03455 2797 . G A 44.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:42:669:0,666:0.995516:44,46,0 +K03455 2848 . T TA 46.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:38:820:85,704:0.858537:46,38,0 +K03455 2874 . C T 36.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:32:777:1,756:0.972973:36,34,0 +K03455 2882 . G T 37.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:33:737:9,721:0.97829:37,34,0 +K03455 2894 . T C 32.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:30:728:1,717:0.98489:32,34,0 +K03455 2906 . C T 32.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:29:653:2,650:0.995406:32,31,0 +K03455 2913 . G A 41.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:39:639:1,638:0.998435:41,42,0 +K03455 2987 . C T 11.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:11:235:0,234:0.995745:11,23,0 +K03455 3020 . A G 0.8 RefCall . GT:GQ:DP:AD:VAF:PL ./.:8:100:0,100:1:0,26,7 +K03455 3042 . A C 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:37:12:9,3:0.25:0,41,39 |
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| diff -r 98fe794d2ec0 -r 918c8b94c8d8 test-data/report.html --- a/test-data/report.html Sun Sep 04 07:54:30 2022 +0000 +++ b/test-data/report.html Mon Apr 10 11:11:16 2023 +0000 |
| [ |
| b'@@ -14,7 +14,7 @@\n <div id="vis"></div>\n <script>\n (function(vegaEmbed) {\n- var spec = {"config": {"view": {"continuousWidth": 400, "continuousHeight": 300}, "header": {"labelFontSize": 16, "titleFontSize": 20}, "title": {"fontSize": 20}}, "vconcat": [{"hconcat": [{"layer": [{"mark": "bar", "encoding": {"color": {"type": "nominal", "field": "label", "legend": null, "scale": {"domain": ["Biallelic_Insertion", "Biallelic_Deletion", "Biallelic_SNP", "Biallelic_MNP", "Multiallelic_Insertion", "Multiallelic_Deletion", "Multiallelic_SNP", "Multiallelic_Complex", "RefCall"], "scheme": "set1"}}, "tooltip": {"type": "quantitative", "field": "value", "format": ".4s"}, "x": {"type": "nominal", "axis": {"labelAngle": -45}, "field": "label", "sort": ["Biallelic_Insertion", "Biallelic_Deletion", "Biallelic_SNP", "Biallelic_MNP", "Multiallelic_Insertion", "Multiallelic_Deletion", "Multiallelic_SNP", "Multiallelic_Complex", "RefCall"], "title": null}, "y": {"type": "quantitative", "axis": {"format": "s", "title": "Count"}, "field": "value"}}}, {"mark": {"type": "text", "dy": -5}, "encoding": {"color": {"type": "nominal", "field": "label", "legend": null, "scale": {"domain": ["Biallelic_Insertion", "Biallelic_Deletion", "Biallelic_SNP", "Biallelic_MNP", "Multiallelic_Insertion", "Multiallelic_Deletion", "Multiallelic_SNP", "Multiallelic_Complex", "RefCall"], "scheme": "set1"}}, "text": {"type": "quantitative", "field": "value", "format": ".4s"}, "tooltip": {"type": "quantitative", "field": "value", "format": ".4s"}, "x": {"type": "nominal", "axis": {"labelAngle": -45}, "field": "label", "sort": ["Biallelic_Insertion", "Biallelic_Deletion", "Biallelic_SNP", "Biallelic_MNP", "Multiallelic_Insertion", "Multiallelic_Deletion", "Multiallelic_SNP", "Multiallelic_Complex", "RefCall"], "title": null}, "y": {"type": "quantitative", "axis": {"format": "s", "title": "Count"}, "field": "value"}}}], "data": {"name": "data-937b261a5c3b87122763fad938b49170"}, "height": 200, "title": "Variant types", "width": 400}, {"data": {"name": "data-b2d3f7df703b341956fcd700e0a250a9"}, "mark": {"type": "bar", "color": "#4a1486"}, "encoding": {"x": {"type": "quantitative", "field": "s", "title": "Depth"}, "x2": {"field": "e"}, "y": {"type": "quantitative", "axis": {"format": "s"}, "field": "c", "stack": true, "title": "Count"}}, "height": 200, "selection": {"selector001": {"type": "interval", "bind": "scales", "encodings": ["x"]}}, "title": "Depth", "width": 200}, {"data": {"name": "data-70a9f9970a7a116b20641236c44085c7"}, "mark": {"type": "bar", "color": "#0c2c84"}, "encoding": {"x": {"type": "quantitative", "field": "s", "scale": {"domain": [0, 150]}, "title": "QUAL"}, "x2": {"field": "e"}, "y": {"type": "quantitative", "axis": {"format": "s"}, "field": "c", "stack": true, "title": "Count"}}, "height": 200, "selection": {"selector002": {"type": "interval", "bind": "scales", "encodings": ["x"]}}, "title": "Quality score", "width": 200}, {"data": {"name": "data-65fbcc082c59672dad70840283183855"}, "mark": {"type": "bar", "color": "#0c2c84"}, "encoding": {"x": {"type": "quantitative", "field": "s", "scale": {"domain": [0, 150]}, "title": "GQ"}, "x2": {"field": "e"}, "y": {"type": "quantitative", "axis": {"format": "s"}, "field": "c", "stack": true, "title": "Count"}}, "height": 200, "selection": {"selector003": {"type": "interval", "bind": "scales", "encodings": ["x"]}}, "title": "Genotype quality", "width": 200}], "resolve": {"scale": {"color": "independent"}}}, {"hconcat": [{"data": {"name": "data-3d9c2f5348720c594baf1c98c0318a7b"}, "facet": {"column": {"type": "nominal", "field": "GT", "sort": ["Ref (0/0)", "Het (0/x)", "Hom (x/x)"], "title": "Main genotypes"}}, "spec": {"layer": [{"mark": "bar", "encoding": {"x": {"type": "quantitative", "field": "s", "title": "VAF"}, "x2": {"field": "e"}, "y": {"type": "quantitative", "axis": {"format": "s"}, "field": "c", "stack": true, "title": "Count"}}}, {"mark": "rule", "encoding": {"x": {"type": "quantitative", "fie'..b'": 0, "GT": "Uncalled (./.)", "g": "others", "l": null}, {"s": 0.22, "e": 0.24, "c": 0, "GT": "Uncalled (./.)", "g": "others", "l": null}, {"s": 0.24, "e": 0.26, "c": 0, "GT": "Uncalled (./.)", "g": "others", "l": null}, {"s": 0.26, "e": 0.28, "c": 0, "GT": "Uncalled (./.)", "g": "others", "l": null}, {"s": 0.28, "e": 0.3, "c": 0, "GT": "Uncalled (./.)", "g": "others", "l": null}, {"s": 0.3, "e": 0.32, "c": 0, "GT": "Uncalled (./.)", "g": "others", "l": null}, {"s": 0.32, "e": 0.34, "c": 0, "GT": "Uncalled (./.)", "g": "others", "l": null}, {"s": 0.34, "e": 0.36, "c": 0, "GT": "Uncalled (./.)", "g": "others", "l": null}, {"s": 0.36, "e": 0.38, "c": 0, "GT": "Uncalled (./.)", "g": "others", "l": null}, {"s": 0.38, "e": 0.4, "c": 0, "GT": "Uncalled (./.)", "g": "others", "l": null}, {"s": 0.4, "e": 0.42, "c": 0, "GT": "Uncalled (./.)", "g": "others", "l": null}, {"s": 0.42, "e": 0.44, "c": 0, "GT": "Uncalled (./.)", "g": "others", "l": null}, {"s": 0.44, 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