# HG changeset patch
# User iuc
# Date 1666778571 0
# Node ID b43df0ce6c8763a365956ca4267064ba0f13bf68
# Parent 27fd1c1f00a8de4d9e3a710eda9800f112bbeca5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2d42622b1aafec3492a8e42a15c52e4b96f55b8b
diff -r 27fd1c1f00a8 -r b43df0ce6c87 ensembl_vep.xml
--- a/ensembl_vep.xml Tue Jun 28 10:41:15 2022 +0000
+++ b/ensembl_vep.xml Wed Oct 26 10:02:51 2022 +0000
@@ -1,375 +1,373 @@
- with VEP
-
- 106.1
- 1
- 106
-
-
-
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-
-
-
- ensembl-vep
- perl-math-cdf
- grep
-
- 'custom_annotation.${custom_ext}.gz' &&
- tabix -p gff 'custom_annotation.${custom_ext}.gz' &&
- #end if
- #if $ref_seq.ref_source == "cached":
- ln -s '$ref_seq.ref.fields.path' reference.fa &&
- #else if $ref_seq.ref_source == "history":
- ln -s '$ref_seq.ref' reference.fa &&
- #end if
-
- vep -i '${annotation_cache.input1}' -o MainOutput.vcf --vcf
- #if $annotation_cache.source == "custom":
- --$custom_ext 'custom_annotation.${custom_ext}.gz'
- #else:
- --cache
- --species '${annotation_cache.cache_file.fields.species}'
- --dir_cache '${annotation_cache.cache_file.fields.path}'
- #if $annotation_cache.cache_file.fields.cachetype == "refseq": --refseq
- #if $annotation_cache.cache_file.fields.cachetype == "merged": --merged
- #if $annotation_cache.cache_file.fields.version != "@DB_VERSION@": --cache_version $annotation_cache.cache_file.fields.version
- ## The --offline flag automatically activates --cache. This is not wanted in our gff/gtf case but also not needed as no internet connection is required for annotating with these custom annotation sources.
- --offline
- #end if
- #if $ref_seq.ref_source != "no_ref"
- --fasta reference.fa
- #end if
- --stats_text
-
- #if $out_opt.sift != "None": --sift $out_opt.sift
- #if $out_opt.polyphen != "None": --polyphen $out_opt.polyphen
- #if $out_opt.nearest != "None": --nearest $out_opt.nearest
- #if int($out_opt.distance_custom.distance_1) > -1:
- --distance $out_opt.distance_custom.distance_1#if int($out_opt.distance_custom.distance_2) > -1: ,$out_opt.distance_custom.distance_2
- #end if
- #if $out_opt.cell_type != "": --cell_type '$out_opt.cell_type'
- #if $out_opt.individual != "": --individual $out_opt.individual
- --vcf_info_field $out_opt.vcf_info_type.vcf_info_field
- --terms $out_opt.terms
- #if $out_opt.out_opt_checkboxes != "None": ${' '.join(str($out_opt.out_opt_checkboxes).split(","))}
- #if $out_opt.shift_var.shift_selector != "None":
- $out_opt.shift_var.shift_selector
- #if $out_opt.shift_var.shift_selector == "--shift_hgvs 0 --shift_3prime 1"
- #if $out_opt.shift_var.shift_length != "None": $out_opt.shift_var.shift_length
- #end if
- #end if
- #if $ident.input_synonyms: --synonyms '${ident.input_synonyms}'
- #if $ident.ident_checkboxes != "None": ${' '.join(str($ident.ident_checkboxes).split(","))}
- #if $colo_var.colo_var_checkboxes != "None": ${' '.join(str($colo_var.colo_var_checkboxes).split(","))}
- #if $fil_qc.fil_qc_checkboxes != "None": ${' '.join(str($fil_qc.fil_qc_checkboxes).split(","))}
- $plugins.carol
- $plugins.condel
- #if $plugins.exacpli_file: --plugin ExACpLI,'${plugins.exacpli_file}'
- #if $plugins.loftool_file: --plugin LoFtool,'${plugins.loftool_file}'
- ]]>
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- 10.1186/s13059-016-0974-4
-
+ with VEP
+
+ 108.0
+ 0
+ 108
+
+
+
+
+
+
+
+
+
+
+
+ ensembl-vep
+ perl-math-cdf
+ grep
+
+ 'custom_annotation.${custom_ext}.gz' &&
+ tabix -p gff 'custom_annotation.${custom_ext}.gz' &&
+ #end if
+ #if $ref_seq.ref_source == "cached":
+ ln -s '$ref_seq.ref.fields.path' reference.fa &&
+ #else if $ref_seq.ref_source == "history":
+ ln -s '$ref_seq.ref' reference.fa &&
+ #end if
+
+ vep -i '${annotation_cache.input1}' -o MainOutput.vcf --vcf
+ #if $annotation_cache.source == "custom":
+ --$custom_ext 'custom_annotation.${custom_ext}.gz'
+ #else:
+ --cache
+ --species '${annotation_cache.cache_file.fields.species}'
+ --dir_cache '${annotation_cache.cache_file.fields.path}'
+ #if $annotation_cache.cache_file.fields.cachetype == "refseq": --refseq
+ #if $annotation_cache.cache_file.fields.cachetype == "merged": --merged
+ #if $annotation_cache.cache_file.fields.version != "@DB_VERSION@": --cache_version $annotation_cache.cache_file.fields.version
+ ## The --offline flag automatically activates --cache. This is not wanted in our gff/gtf case but also not needed as no internet connection is required for annotating with these custom annotation sources.
+ --offline
+ #end if
+ #if $ref_seq.ref_source != "no_ref"
+ --fasta reference.fa
+ #end if
+ --stats_text
+
+ #if $out_opt.sift != "None": --sift $out_opt.sift
+ #if $out_opt.polyphen != "None": --polyphen $out_opt.polyphen
+ #if $out_opt.nearest != "None": --nearest $out_opt.nearest
+ #if int($out_opt.distance_custom.distance_1) > -1:
+ --distance $out_opt.distance_custom.distance_1#if int($out_opt.distance_custom.distance_2) > -1: ,$out_opt.distance_custom.distance_2
+ #end if
+ #if $out_opt.cell_type != "": --cell_type '$out_opt.cell_type'
+ #if $out_opt.individual != "": --individual $out_opt.individual
+ --vcf_info_field $out_opt.vcf_info_type.vcf_info_field
+ --terms $out_opt.terms
+ #if $out_opt.out_opt_checkboxes != "None": ${' '.join(str($out_opt.out_opt_checkboxes).split(","))}
+ #if $out_opt.shift_var.shift_selector != "None":
+ $out_opt.shift_var.shift_selector
+ #if $out_opt.shift_var.shift_selector == "--shift_hgvs 0 --shift_3prime 1"
+ #if $out_opt.shift_var.shift_length != "None": $out_opt.shift_var.shift_length
+ #end if
+ #end if
+ #if $ident.input_synonyms: --synonyms '${ident.input_synonyms}'
+ #if $ident.ident_checkboxes != "None": ${' '.join(str($ident.ident_checkboxes).split(","))}
+ #if $colo_var.colo_var_checkboxes != "None": ${' '.join(str($colo_var.colo_var_checkboxes).split(","))}
+ #if $fil_qc.fil_qc_checkboxes != "None": ${' '.join(str($fil_qc.fil_qc_checkboxes).split(","))}
+ $plugins.carol
+ $plugins.condel
+ #if $plugins.exacpli_file: --plugin ExACpLI,'${plugins.exacpli_file}'
+ #if $plugins.loftool_file: --plugin LoFtool,'${plugins.loftool_file}'
+ ]]>
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+ 10.1186/s13059-016-0974-4
+
diff -r 27fd1c1f00a8 -r b43df0ce6c87 test-data/output_test1.vcf
--- a/test-data/output_test1.vcf Tue Jun 28 10:41:15 2022 +0000
+++ b/test-data/output_test1.vcf Wed Oct 26 10:02:51 2022 +0000
@@ -1,5 +1,4 @@
##fileformat=VCFv4.0
-##VEP="v105" time="2022-03-07 13:29:51" cache="/home/sebastian/.planemo/planemo_tmp_fhheutk7/test-data/test-cache/drosophila_melanogaster/105_BDGP6.32" db="drosophila_melanogaster_core_105_9@ensembldb.ensembl.org" ensembl-io=105.2a0a40c ensembl-variation=105.ac8178e ensembl=105.525fbcb ensembl-funcgen=105.660df8f assembly="BDGP6.32" genebuild="dmel_r6.32_FB2020_01"
##INFO=
#CHROM POS ID REF ALT QUAL FILTER INFO
chrM 5701 . GA G . . CSQ=-|downstream_gene_variant|MODIFIER|mt:ND2|FBgn0013680|Transcript|FBtr0100857|protein_coding|||||||||||4439|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:tRNA:Trp-TCA|FBgn0013709|Transcript|FBtr0100858|tRNA|||||||||||4373|1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:tRNA:Cys-GCA|FBgn0013690|Transcript|FBtr0100859|tRNA|||||||||||4319|-1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:tRNA:Tyr-GTA|FBgn0013710|Transcript|FBtr0100860|tRNA|||||||||||4234|-1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:CoI|FBgn0013674|Transcript|FBtr0100861|protein_coding|||||||||||2693|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:tRNA:Leu-TAA|FBgn0013699|Transcript|FBtr0100862|tRNA|||||||||||2625|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:CoII|FBgn0013675|Transcript|FBtr0100863|protein_coding|||||||||||1935|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:tRNA:Lys-CTT|FBgn0013697|Transcript|FBtr0100864|tRNA|||||||||||1864|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:tRNA:Asp-GTC|FBgn0013691|Transcript|FBtr0100865|tRNA|||||||||||1796|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:ATPase8|FBgn0013673|Transcript|FBtr0100866|protein_coding|||||||||||1634|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:CoIII|FBgn0013676|Transcript|FBtr0100868|protein_coding|||||||||||178|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:tRNA:Gly-TCC|FBgn0013694|Transcript|FBtr0100869|tRNA|||||||||||95|1||FlyBaseName_gene|,-|frameshift_variant|HIGH|mt:ND3|FBgn0013681|Transcript|FBtr0100870|protein_coding|1/1||||95|95|32|D/X|gAc/gc|||1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:tRNA:Ala-TGC|FBgn0013689|Transcript|FBtr0100871|tRNA|||||||||||281|1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:tRNA:Arg-TCG|FBgn0013704|Transcript|FBtr0100872|tRNA|||||||||||360|1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:tRNA:Asn-GTT|FBgn0013701|Transcript|FBtr0100873|tRNA|||||||||||424|1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:tRNA:Ser-GCT|FBgn0013705|Transcript|FBtr0100874|tRNA|||||||||||489|1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:tRNA:Glu-TTC|FBgn0013692|Transcript|FBtr0100875|tRNA|||||||||||557|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:tRNA:Phe-GAA|FBgn0013693|Transcript|FBtr0100876|tRNA|||||||||||642|-1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:tRNA:His-GTG|FBgn0013695|Transcript|FBtr0100878|tRNA|||||||||||2439|-1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:ND4L|FBgn0013683|Transcript|FBtr0100880|protein_coding|||||||||||3843|-1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:tRNA:Thr-TGT|FBgn0013707|Transcript|FBtr0100881|tRNA|||||||||||4136|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:tRNA:Pro-TGG|FBgn0013702|Transcript|FBtr0100882|tRNA|||||||||||4202|-1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:ND6|FBgn0013685|Transcript|FBtr0100883|protein_coding|||||||||||4269|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:ATPase6|FBgn0013672|Transcript|FBtr0433498|protein_coding|||||||||||966|1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:ND4|FBgn0262952|Transcript|FBtr0433500|protein_coding|||||||||||2505|-1||FlyBaseName_gene|,-|downstream_gene_variant|MODIFIER|mt:ND5|FBgn0013684|Transcript|FBtr0433501|protein_coding|||||||||||707|-1||FlyBaseName_gene|,-|upstream_gene_variant|MODIFIER|mt:Cyt-b|FBgn0013678|Transcript|FBtr0433502|protein_coding|||||||||||4797|1||FlyBaseName_gene|
diff -r 27fd1c1f00a8 -r b43df0ce6c87 test-data/output_test2.vcf
--- a/test-data/output_test2.vcf Tue Jun 28 10:41:15 2022 +0000
+++ b/test-data/output_test2.vcf Wed Oct 26 10:02:51 2022 +0000
@@ -4,8 +4,7 @@
##ALT=
##INFO=
##INFO=
-##VEP="v105" time="2022-03-30 19:24:59" ensembl=105.525fbcb ensembl-io=105.2a0a40c ensembl-funcgen=105.660df8f ensembl-variation=105.ac8178e
##INFO=
-##INFO=
+##INFO=
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096
21 5733 rs142513484 C T . . CSQ=T|3_prime_UTR_variant|MODIFIER|MRPL39|ENSG00000154719|Transcript|ENST00000307301|protein_coding|3/3||||159|||||||-1||||custom_annotation.gtf.gz|,T|missense_variant|MODERATE|MRPL39|ENSG00000154719|Transcript|ENST00000352957|protein_coding|2/2||||70|70|24|A/T|Gca/Aca|||-1||||custom_annotation.gtf.gz|,T|upstream_gene_variant|MODIFIER|AP000223.42|ENSG00000260583|Transcript|ENST00000567517|antisense|||||||||||2407|-1||||custom_annotation.gtf.gz| GT 0|0