# HG changeset patch
# User iuc
# Date 1662278070 0
# Node ID 98fe794d2ec0ff8c3c64c2fd44a2225988c76e75
# Parent  b778a18bd878bddc5e337ab6cc9e61409c7f036b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 4255237ed7a51299e25bd7de7ad52ac5d419a56c

diff -r b778a18bd878 -r 98fe794d2ec0 deepvariant.xml
--- a/deepvariant.xml	Fri Oct 01 07:46:42 2021 +0000
+++ b/deepvariant.xml	Sun Sep 04 07:54:30 2022 +0000
@@ -134,12 +134,12 @@
             <output name="vcf_file" ftype="vcf">
                 <assert_contents>
                     <has_text text="##fileformat=VCFv4.2"/>
-                    <has_size value="1846"/>
+                    <has_size value="1842"/>
                 </assert_contents>
             </output>
             <output name="html_report" ftype="html">
                 <assert_contents>
-                    <has_size value="18864" delta="100"/>
+                    <has_size value="14880" delta="100"/>
                 </assert_contents>
             </output>
         </test>
@@ -153,17 +153,17 @@
             <param name="model_type" value="WGS"/>
             <conditional name="regions_conditional">
                 <param name="regions_option" value="bed"/>
-                <param name="bed_file" value="region.bed"/>
+                <param name="bed_file" value="region.bed" ftype="bed"/>
             </conditional>
             <output name="vcf_file" ftype="vcf">
                 <assert_contents>
                     <has_text text="##fileformat=VCFv4.2"/>
-                    <has_size value="1846"/>
+                    <has_size value="1842"/>
                 </assert_contents>
             </output>
             <output name="html_report" ftype="html">
                 <assert_contents>
-                    <has_size value="18864" delta="100"/>
+                    <has_size value="14880" delta="100"/>
                 </assert_contents>
             </output>
         </test>
@@ -183,18 +183,18 @@
             <output name="vcf_file" ftype="vcf">
                 <assert_contents>
                     <has_text text="##fileformat=VCFv4.2"/>
-                    <has_size value="1846"/>
+                    <has_size value="1842"/>
                 </assert_contents>
             </output>
             <output name="gvcf_file" file="output.g.vcf" ftype="vcf">
                 <assert_contents>
                     <has_text text="##fileformat=VCFv4.2"/>
-                    <has_size value="3195"/>
+                    <has_size value="3191"/>
                 </assert_contents>
             </output>
             <output name="html_report" ftype="html">
                 <assert_contents>
-                    <has_size value="18864" delta="100"/>
+                    <has_size value="14880" delta="100"/>
                 </assert_contents>
             </output>
         </test>
diff -r b778a18bd878 -r 98fe794d2ec0 macros.xml
--- a/macros.xml	Fri Oct 01 07:46:42 2021 +0000
+++ b/macros.xml	Sun Sep 04 07:54:30 2022 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.2.0</token>
-    <token name="@SUFFIX_VERSION@">1</token>
+    <token name="@TOOL_VERSION@">1.4.0</token>
+    <token name="@SUFFIX_VERSION@">0</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
             <edam_topic>topic_0199</edam_topic>
diff -r b778a18bd878 -r 98fe794d2ec0 test-data/output.g.vcf
--- a/test-data/output.g.vcf	Fri Oct 01 07:46:42 2021 +0000
+++ b/test-data/output.g.vcf	Sun Sep 04 07:54:30 2022 +0000
@@ -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=1.2.0
+##DeepVariant_version=1.4.0
 ##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,<*>	5.5	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:5:2:0,2,0:1,0:3,15,0,990,990,990
+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	2607	.	A	<*>	0	.	END=2607	GT:GQ:MIN_DP:PL	0/0:6:2:0,6,59
-K03455	2608	.	A	T,<*>	7.8	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:7:2:0,2,0:1,0:6,14,0,990,990,990
-K03455	2609	.	A	T,<*>	4.8	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:4:2:0,2,0:1,0:2,14,0,990,990,990
+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	2610	.	G	<*>	0	.	END=2612	GT:GQ:MIN_DP:PL	0/0:6:2:0,6,59
-K03455	2613	.	A	T,<*>	1.1	RefCall	.	GT:GQ:DP:AD:VAF:PL	./.:7:2:0,2,0:1,0:0,19,5,990,990,990
+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	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,<*>	20.1	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:20:201:0,201,0:1,0:20,47,0,990,990,990
+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	2653	.	T	<*>	0	.	END=2659	GT:GQ:MIN_DP:PL	0/0:50:201:0,300,2999
-K03455	2660	.	T	C,<*>	25.5	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:25:213:0,213,0:1,0:25,45,0,990,990,990
+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	2661	.	T	<*>	0	.	END=2663	GT:GQ:MIN_DP:PL	0/0:50:213:0,300,2999
-K03455	2664	.	A	G,<*>	21.3	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:21:238:0,238,0:1,0:21,45,0,990,990,990
+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	2665	.	C	<*>	0	.	END=2668	GT:GQ:MIN_DP:PL	0/0:50:240:0,300,2999
-K03455	2669	.	G	A,<*>	20.6	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:21:250:0,250,0:1,0:20,42,0,990,990,990
+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
diff -r b778a18bd878 -r 98fe794d2ec0 test-data/output.vcf
--- a/test-data/output.vcf	Fri Oct 01 07:46:42 2021 +0000
+++ b/test-data/output.vcf	Sun Sep 04 07:54:30 2022 +0000
@@ -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=1.2.0
+##DeepVariant_version=1.4.0
 ##contig=<ID=K03455,length=9719>
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SRR8525881
-K03455	2652	.	G	A	23.7	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:24:201:0,200:0.995025:23,45,0
-K03455	2660	.	T	C	25.3	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:25:213:0,213:1:25,45,0
-K03455	2664	.	A	G	21.4	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:21:238:0,238:1:21,45,0
-K03455	2669	.	G	A	20.3	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:20:258:0,250:0.968992:20,43,0
-K03455	2720	.	T	C	31.9	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:32:384:0,380:0.989583:31,47,0
-K03455	2797	.	G	A	39.4	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:39:669:0,666:0.995516:39,54,0
-K03455	2848	.	T	TA	41.3	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:39:820:85,704:0.858537:41,43,0
-K03455	2874	.	C	T	32	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:32:777:1,756:0.972973:32,45,0
-K03455	2882	.	G	T	33.2	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:33:737:9,721:0.97829:33,49,0
-K03455	2894	.	T	C	28.2	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:28:728:1,717:0.98489:28,51,0
-K03455	2906	.	C	T	23.7	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:24:653:2,650:0.995406:23,53,0
-K03455	2913	.	G	A	27.4	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:27:639:1,638:0.998435:27,53,0
-K03455	2987	.	C	T	16.5	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:16:235:0,234:0.995745:16,38,0
-K03455	3020	.	A	G	3.5	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:3:100:0,100:1:0,24,0
-K03455	3042	.	A	C	0	RefCall	.	GT:GQ:DP:AD:VAF:PL	0/0:37:12:9,3:0.25:0,40,39
+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
diff -r b778a18bd878 -r 98fe794d2ec0 test-data/report.html
--- a/test-data/report.html	Fri Oct 01 07:46:42 2021 +0000
+++ b/test-data/report.html	Sun Sep 04 07:54:30 2022 +0000
@@ -14,7 +14,7 @@
   <div id="vis"></div>
   <script>
     (function(vegaEmbed) {
-      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-1fdc69f1e562b859232e2c7c67fa0330"}, "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-2eb03df08bc1de8ab65cb5fa9b73d2ca"}, "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", "field": "l"}}}], "height": 200, "width": 200}, "resolve": {"scale": {"y": "independent"}}}, {"data": {"name": "data-c27c47333ad35eb954c1fa8cd921aa87"}, "mark": "bar", "encoding": {"column": {"type": "nominal", "field": "GT", "title": "Other genotypes"}, "x": {"type": "quantitative", "field": "s", "title": "VAF"}, "x2": {"field": "e"}, "y": {"type": "quantitative", "axis": {"format": "s"}, "field": "c", "stack": true, "title": "Count"}}, "height": 150, "resolve": {"scale": {"y": "independent"}}, "width": 150}]}, {"hconcat": [{"data": {"name": "data-da9c8bf99f8c1b3dd20c5e4c1ba410e4"}, "facet": {"column": {"type": "nominal", "field": "ref", "sort": ["A", "G", "T", "C"], "title": "Biallelic base changes from reference"}}, "spec": {"layer": [{"mark": "bar", "encoding": {"color": {"type": "nominal", "field": "alt", "legend": null, "scale": {"domain": ["A", "G", "T", "C"], "scheme": "category20"}, "sort": ["A", "G", "T", "C"]}, "tooltip": {"type": "quantitative", "field": "count", "format": ".4s"}, "x": {"type": "nominal", "field": "alt", 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