Mercurial > repos > iuc > ensembl_vep

comparison ensembl_vep.xml @ 2:b43df0ce6c87 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 2d42622b1aafec3492a8e42a15c52e4b96f55b8b
author iuc
date Wed, 26 Oct 2022 10:02:51 +0000
parents 27fd1c1f00a8
children ff0a8cda0c0b
comparison
equal deleted inserted replaced
1:27fd1c1f00a8 2:b43df0ce6c87
1 <tool id="ensembl_vep" name="Predict variant effects" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="ensembl_vep" name="Predict variant effects" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>with VEP</description> 2 <description>with VEP</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">106.1</token> 4 <token name="@TOOL_VERSION@">108.0</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 <token name="@DB_VERSION@">106</token> 6 <token name="@DB_VERSION@">108</token>
7 <xml name="vcf_input"> 7 <xml name="vcf_input">
8 <param type="data" name="input1" label="VCF input file" format="vcf"> 8 <param type="data" name="input1" label="VCF input file" format="vcf">
9 <validator type="unspecified_build" /> 9 <validator type="unspecified_build" />
10 <yield /> 10 <yield />
11 </param> 11 </param>
12 </xml> 12 </xml>
13 <xml name="vcf_input_validation"> 13 <xml name="vcf_input_validation">
14 <validator type="dataset_metadata_in_data_table" table_name="vep_versioned_annotation_cache" metadata_name="dbkey" metadata_column="1" message="No annotation caches are available for the specified build" /> 14 <validator type="dataset_metadata_in_data_table" table_name="vep_versioned_annotation_cache" metadata_name="dbkey" metadata_column="1" message="No annotation caches are available for the specified build" />
15 </xml> 15 </xml>
16 </macros> 16 </macros>
17 <requirements> 17 <requirements>
18 <requirement type="package" version="@TOOL_VERSION@">ensembl-vep</requirement> 18 <requirement type="package" version="@TOOL_VERSION@">ensembl-vep</requirement>
19 <requirement type="package" version="0.1">perl-math-cdf</requirement> 19 <requirement type="package" version="0.1">perl-math-cdf</requirement>
20 <requirement type="package" version="3.4">grep</requirement> 20 <requirement type="package" version="3.4">grep</requirement>
21 </requirements> 21 </requirements>
22 <command detect_errors="exit_code"><![CDATA[ 22 <command detect_errors="exit_code"><![CDATA[
23 #if $annotation_cache.source == "custom": 23 #if $annotation_cache.source == "custom":
24 #set $custom_ext = $annotation_cache.custom_annotation.ext[:3] 24 #set $custom_ext = $annotation_cache.custom_annotation.ext[:3]
25 set -o pipefail && 25 set -o pipefail &&
26 grep -v "#" '${annotation_cache.custom_annotation}' | 26 grep -v "#" '${annotation_cache.custom_annotation}' |
27 LC_ALL=C sort -k1,1 -k4,4n -k5,5n -t$'\t' | 27 LC_ALL=C sort -k1,1 -k4,4n -k5,5n -t$'\t' |
28 bgzip -c > 'custom_annotation.${custom_ext}.gz' && 28 bgzip -c > 'custom_annotation.${custom_ext}.gz' &&
29 tabix -p gff 'custom_annotation.${custom_ext}.gz' && 29 tabix -p gff 'custom_annotation.${custom_ext}.gz' &&
30 #end if 30 #end if
31 #if $ref_seq.ref_source == "cached": 31 #if $ref_seq.ref_source == "cached":
32 ln -s '$ref_seq.ref.fields.path' reference.fa && 32 ln -s '$ref_seq.ref.fields.path' reference.fa &&
33 #else if $ref_seq.ref_source == "history": 33 #else if $ref_seq.ref_source == "history":
34 ln -s '$ref_seq.ref' reference.fa && 34 ln -s '$ref_seq.ref' reference.fa &&
35 #end if 35 #end if
36 36
37 vep -i '${annotation_cache.input1}' -o MainOutput.vcf --vcf 37 vep -i '${annotation_cache.input1}' -o MainOutput.vcf --vcf
38 #if $annotation_cache.source == "custom": 38 #if $annotation_cache.source == "custom":
39 --$custom_ext 'custom_annotation.${custom_ext}.gz' 39 --$custom_ext 'custom_annotation.${custom_ext}.gz'
40 #else: 40 #else:
41 --cache 41 --cache
42 --species '${annotation_cache.cache_file.fields.species}' 42 --species '${annotation_cache.cache_file.fields.species}'
43 --dir_cache '${annotation_cache.cache_file.fields.path}' 43 --dir_cache '${annotation_cache.cache_file.fields.path}'
44 #if $annotation_cache.cache_file.fields.cachetype == "refseq": --refseq 44 #if $annotation_cache.cache_file.fields.cachetype == "refseq": --refseq
45 #if $annotation_cache.cache_file.fields.cachetype == "merged": --merged 45 #if $annotation_cache.cache_file.fields.cachetype == "merged": --merged
46 #if $annotation_cache.cache_file.fields.version != "@DB_VERSION@": --cache_version $annotation_cache.cache_file.fields.version 46 #if $annotation_cache.cache_file.fields.version != "@DB_VERSION@": --cache_version $annotation_cache.cache_file.fields.version
47 ## 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. 47 ## 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.
48 --offline 48 --offline
49 #end if 49 #end if
50 #if $ref_seq.ref_source != "no_ref" 50 #if $ref_seq.ref_source != "no_ref"
51 --fasta reference.fa 51 --fasta reference.fa
52 #end if 52 #end if
53 --stats_text 53 --stats_text
54 54
55 #if $out_opt.sift != "None": --sift $out_opt.sift 55 #if $out_opt.sift != "None": --sift $out_opt.sift
56 #if $out_opt.polyphen != "None": --polyphen $out_opt.polyphen 56 #if $out_opt.polyphen != "None": --polyphen $out_opt.polyphen
57 #if $out_opt.nearest != "None": --nearest $out_opt.nearest 57 #if $out_opt.nearest != "None": --nearest $out_opt.nearest
58 #if int($out_opt.distance_custom.distance_1) > -1: 58 #if int($out_opt.distance_custom.distance_1) > -1:
59 --distance $out_opt.distance_custom.distance_1#if int($out_opt.distance_custom.distance_2) > -1: ,$out_opt.distance_custom.distance_2 59 --distance $out_opt.distance_custom.distance_1#if int($out_opt.distance_custom.distance_2) > -1: ,$out_opt.distance_custom.distance_2
60 #end if 60 #end if
61 #if $out_opt.cell_type != "": --cell_type '$out_opt.cell_type' 61 #if $out_opt.cell_type != "": --cell_type '$out_opt.cell_type'
62 #if $out_opt.individual != "": --individual $out_opt.individual 62 #if $out_opt.individual != "": --individual $out_opt.individual
63 --vcf_info_field $out_opt.vcf_info_type.vcf_info_field 63 --vcf_info_field $out_opt.vcf_info_type.vcf_info_field
64 --terms $out_opt.terms 64 --terms $out_opt.terms
65 #if $out_opt.out_opt_checkboxes != "None": ${' '.join(str($out_opt.out_opt_checkboxes).split(","))} 65 #if $out_opt.out_opt_checkboxes != "None": ${' '.join(str($out_opt.out_opt_checkboxes).split(","))}
66 #if $out_opt.shift_var.shift_selector != "None": 66 #if $out_opt.shift_var.shift_selector != "None":
67 $out_opt.shift_var.shift_selector 67 $out_opt.shift_var.shift_selector
68 #if $out_opt.shift_var.shift_selector == "--shift_hgvs 0 --shift_3prime 1" 68 #if $out_opt.shift_var.shift_selector == "--shift_hgvs 0 --shift_3prime 1"
69 #if $out_opt.shift_var.shift_length != "None": $out_opt.shift_var.shift_length 69 #if $out_opt.shift_var.shift_length != "None": $out_opt.shift_var.shift_length
70 #end if 70 #end if
71 #end if 71 #end if
72 #if $ident.input_synonyms: --synonyms '${ident.input_synonyms}' 72 #if $ident.input_synonyms: --synonyms '${ident.input_synonyms}'
73 #if $ident.ident_checkboxes != "None": ${' '.join(str($ident.ident_checkboxes).split(","))} 73 #if $ident.ident_checkboxes != "None": ${' '.join(str($ident.ident_checkboxes).split(","))}
74 #if $colo_var.colo_var_checkboxes != "None": ${' '.join(str($colo_var.colo_var_checkboxes).split(","))} 74 #if $colo_var.colo_var_checkboxes != "None": ${' '.join(str($colo_var.colo_var_checkboxes).split(","))}
75 #if $fil_qc.fil_qc_checkboxes != "None": ${' '.join(str($fil_qc.fil_qc_checkboxes).split(","))} 75 #if $fil_qc.fil_qc_checkboxes != "None": ${' '.join(str($fil_qc.fil_qc_checkboxes).split(","))}
76 $plugins.carol 76 $plugins.carol
77 $plugins.condel 77 $plugins.condel
78 #if $plugins.exacpli_file: --plugin ExACpLI,'${plugins.exacpli_file}' 78 #if $plugins.exacpli_file: --plugin ExACpLI,'${plugins.exacpli_file}'
79 #if $plugins.loftool_file: --plugin LoFtool,'${plugins.loftool_file}' 79 #if $plugins.loftool_file: --plugin LoFtool,'${plugins.loftool_file}'
80 ]]></command> 80 ]]></command>
81 <inputs> 81 <inputs>
82 <conditional name="annotation_cache"> 82 <conditional name="annotation_cache">
83 <param name="source" type="select" label="Select source of annotation data" help="Ensembl strongly recommends to only use annotation cache files with a version number matching the VEP version. You can disable the corresponding filtering of available cache files at your own risk. This does not apply if you select a GFF/GTF annotation source."> 83 <param name="source" type="select" label="Select source of annotation data" help="Ensembl strongly recommends to only use annotation cache files with a version number matching the VEP version. You can disable the corresponding filtering of available cache files at your own risk. This does not apply if you select a GFF/GTF annotation source.">
84 <option value="restricted">VEP cache file with matching version number</option> 84 <option value="restricted">VEP cache file with matching version number</option>
85 <option value="unrestricted">Any VEP cache file</option> 85 <option value="unrestricted">Any VEP cache file</option>
86 <option value="custom">GFF or GTF from history</option> 86 <option value="custom">GFF or GTF from history</option>
87 </param> 87 </param>
88 <when value="restricted"> 88 <when value="restricted">
89 <expand macro="vcf_input"> 89 <expand macro="vcf_input">
90 <expand macro="vcf_input_validation" /> 90 <expand macro="vcf_input_validation" />
91 </expand> 91 </expand>
92 <param name="cache_file" type="select" label="Select annotation cache file" help="If the annotation data of interest is not listed, have a look at all available cache files regardless of their version number or contact your Galaxy admin."> 92 <param name="cache_file" type="select" label="Select annotation cache file" help="If the annotation data of interest is not listed, have a look at all available cache files regardless of their version number or contact your Galaxy admin.">
93 <options from_data_table="vep_versioned_annotation_cache"> 93 <options from_data_table="vep_versioned_annotation_cache">
94 <filter type="static_value" value="@DB_VERSION@" column="2" /> 94 <filter type="static_value" value="@DB_VERSION@" column="2" />
95 <filter type="sort_by" column="4"/> 95 <filter type="sort_by" column="4"/>
96 </options> 96 </options>
97 <validator type="no_options" message="No annotation caches are available"/> 97 <validator type="no_options" message="No annotation caches are available"/>
98 </param> 98 </param>
99 </when> 99 </when>
100 <when value="unrestricted"> 100 <when value="unrestricted">
101 <expand macro="vcf_input"> 101 <expand macro="vcf_input">
102 <expand macro="vcf_input_validation" /> 102 <expand macro="vcf_input_validation" />
103 </expand> 103 </expand>
104 <param name="cache_file" type="select" label="Select annotation cache file" help="If the annotation data of interest is not listed, contact your Galaxy admin."> 104 <param name="cache_file" type="select" label="Select annotation cache file" help="If the annotation data of interest is not listed, contact your Galaxy admin.">
105 <options from_data_table="vep_versioned_annotation_cache"> 105 <options from_data_table="vep_versioned_annotation_cache">
106 <filter type="sort_by" column="4"/> 106 <filter type="sort_by" column="4"/>
107 </options> 107 </options>
108 <validator type="no_options" message="No annotation caches are available"/> 108 <validator type="no_options" message="No annotation caches are available"/>
109 </param> 109 </param>
110 </when> 110 </when>
111 <when value="custom"> 111 <when value="custom">
112 <expand macro="vcf_input" /> 112 <expand macro="vcf_input" />
113 <param name="custom_annotation" type="data" format="gff,gtf" label="Select GFF or GTF annotation file from history" help="Choosing this option requires that you also supply a Fasta file as reference genome." /> 113 <param name="custom_annotation" type="data" format="gff,gtf" label="Select GFF or GTF annotation file from history" help="Choosing this option requires that you also supply a Fasta file as reference genome." />
114 </when> 114 </when>
115 </conditional> 115 </conditional>
116 <conditional name="ref_seq"> 116 <conditional name="ref_seq">
117 <param name="ref_source" type="select" label="Use FASTA file as reference sequence (optional)" help="Must be specified if using a GFF/GTF annotation source or if fetching HGVS or SPDI notations."> 117 <param name="ref_source" type="select" label="Use FASTA file as reference sequence (optional)" help="Must be specified if using a GFF/GTF annotation source or if fetching HGVS or SPDI notations.">
118 <option value="no_ref">Do not use extra reference sequence</option> 118 <option value="no_ref">Do not use extra reference sequence</option>
119 <option value="cached">Locally cached</option> 119 <option value="cached">Locally cached</option>
120 <option value="history">History</option> 120 <option value="history">History</option>
121 </param> 121 </param>
122 <when value="no_ref" /> 122 <when value="no_ref" />
123 <when value="cached"> 123 <when value="cached">
124 <param name="ref" type="select" label="Select reference sequence"> 124 <param name="ref" type="select" label="Select reference sequence">
125 <options from_data_table="fasta_indexes"> 125 <options from_data_table="fasta_indexes">
126 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> 126 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
127 </options> 127 </options>
128 </param> 128 </param>
129 </when> 129 </when>
130 <when value="history"> 130 <when value="history">
131 <param name="ref" type="data" format="fasta" label="Select reference sequence" /> 131 <param name="ref" type="data" format="fasta" label="Select reference sequence" />
132 </when> 132 </when>
133 </conditional> 133 </conditional>
134 <section name="out_opt" title="Output options"> 134 <section name="out_opt" title="Output options">
135 <param argument="--sift" type="select" optional="true" label="Output SIFT prediction" help="SIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids."> 135 <param argument="--sift" type="select" optional="true" label="Output SIFT prediction" help="SIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids.">
136 <option value="p">Prediction term only</option> 136 <option value="p">Prediction term only</option>
137 <option value="s">Score only</option> 137 <option value="s">Score only</option>
138 <option value="b">Both</option> 138 <option value="b">Both</option>
139 </param> 139 </param>
140 <param argument="--polyphen" type="select" optional="true" label="Output PolyPhen prediction" help="PolyPhen is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. VEP uses the humVar score by default."> 140 <param argument="--polyphen" type="select" optional="true" label="Output PolyPhen prediction" help="PolyPhen is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. VEP uses the humVar score by default.">
141 <option value="p">Prediction term only</option> 141 <option value="p">Prediction term only</option>
142 <option value="s">Score only</option> 142 <option value="s">Score only</option>
143 <option value="b">Both</option> 143 <option value="b">Both</option>
144 </param> 144 </param>
145 <param argument="--nearest" type="select" optional="true" label="Retrieve transcript or gene with nearest TSS to each input variant" help="Retrieve the transcript or gene with the nearest protein-coding transcription start site (TSS) to each input variant. Note that the nearest TSS may not belong to a transcript that overlaps the input variant, and more than one may be reported in the case where two are equidistant from the input coordinates."> 145 <param argument="--nearest" type="select" optional="true" label="Retrieve transcript or gene with nearest TSS to each input variant" help="Retrieve the transcript or gene with the nearest protein-coding transcription start site (TSS) to each input variant. Note that the nearest TSS may not belong to a transcript that overlaps the input variant, and more than one may be reported in the case where two are equidistant from the input coordinates.">
146 <option value="transcript">Nearest transcript ID</option> 146 <option value="transcript">Nearest transcript ID</option>
147 <option value="gene">Nearest gene ID</option> 147 <option value="gene">Nearest gene ID</option>
148 <option value="symbol">Nearest gene symbol</option> 148 <option value="symbol">Nearest gene symbol</option>
149 </param> 149 </param>
150 150 <conditional name="distance_custom">
151 <conditional name="distance_custom"> 151 <param name="distance_custom_selector" type="select" label="Modify the distance up and/or downstream between a variant and a transcript for which VEP will assign the upstream_gene_variant or downstream_gene_variant consequences" help="Default: 5000. Upstream is 5' and downstream 3' direction. (--distance [bp_distance(,downstream_distance_if_different)])">
152 <param name="distance_custom_selector" type="select" label="Modify the distance up and/or downstream between a variant and a transcript for which VEP will assign the upstream_gene_variant or downstream_gene_variant consequences" help="Default: 5000. Upstream is 5' and downstream 3' direction. (--distance [bp_distance(,downstream_distance_if_different)])"> 152 <option value="default" selected="true">Default</option>
153 <option value="default" selected="true">Default</option> 153 <option value="one_dist">Custom distance used for both upstream and downstream</option>
154 <option value="one_dist">Custom distance used for both upstream and downstream</option> 154 <option value="two_dist">Custom upstream distance and different custom downstream distance</option>
155 <option value="two_dist">Custom upstream distance and different custom downstream distance</option> 155 </param>
156 </param> 156 <when value="default">
157 <when value="default"> 157 <param name="distance_1" type="hidden" value="-1"/>
158 <param name="distance_1" type="hidden" value="-1"/> 158 <param name="distance_2" type="hidden" value="-1"/>
159 <param name="distance_2" type="hidden" value="-1"/> 159 </when>
160 </when> 160 <when value="one_dist">
161 <when value="one_dist"> 161 <param name="distance_1" type="integer" min="0" value="5000" label="Enter custom upstream and downstream distance"/>
162 <param name="distance_1" type="integer" min="0" value="5000" label="Enter custom upstream and downstream distance"/> 162 <param name="distance_2" type="hidden" value="-1"/>
163 <param name="distance_2" type="hidden" value="-1"/> 163 </when>
164 </when> 164 <when value="two_dist">
165 <when value="two_dist"> 165 <param name="distance_1" type="integer" min="0" value="5000" label="Enter custom upstream distance"/>
166 <param name="distance_1" type="integer" min="0" value="5000" label="Enter custom upstream distance"/> 166 <param name="distance_2" type="integer" min="0" value="5000" label="Enter custom downstream distance"/>
167 <param name="distance_2" type="integer" min="0" value="5000" label="Enter custom downstream distance"/> 167 </when>
168 </when> 168 </conditional>
169 </conditional> 169 <param name="cell_type" type="text" optional="true" label="Report only regulatory regions that are found in the given cell type(s):" help="Recommended for advanced users only. Can be a single cell type or a comma-separated list. The functional type in each cell type is reported under CELL_TYPE in the output. (--cell_type)"/>
170 170 <param name="individual" type="text" optional="true" label="Consider only alternate alleles present in the genotypes of the specified individual(s):" help="Enter the individual's IDs as comma-separated list. Individual variant combinations homozygous for the given reference allele will not be reported. Each individual and variant combination is given on a separate line of output. Only works with VCF files containing individual genotype data. (--individual [ind list])" />
171 <param name="cell_type" type="text" optional="true" label="Report only regulatory regions that are found in the given cell type(s):" help="Recommended for advanced users only. Can be a single cell type or a comma-separated list. The functional type in each cell type is reported under CELL_TYPE in the output. (--cell_type)"/> 171 <conditional name="vcf_info_type">
172 <param name="individual" type="text" optional="true" label="Consider only alternate alleles present in the genotypes of the specified individual(s):" help="Enter the individual's IDs as comma-separated list. Individual variant combinations homozygous for the given reference allele will not be reported. Each individual and variant combination is given on a separate line of output. Only works with VCF files containing individual genotype data. (--individual [ind list])" /> 172 <param name="vcf_info_type_selector" type="select" label="Change name of the consequences INFO column in VCF output" help="Default: CSQ. Use ANN for compatibility with other tools such as snpEff (--vcf_info_field [CSQ|ANN|(other)])">
173 <conditional name="vcf_info_type"> 173 <option value="csq" selected="true">CSQ</option>
174 <param name="vcf_info_type_selector" type="select" label="Change name of the consequences INFO column in VCF output" help="Default: CSQ. Use ANN for compatibility with other tools such as snpEff (--vcf_info_field [CSQ|ANN|(other)])"> 174 <option value="ann">ANN</option>
175 <option value="csq" selected="true">CSQ</option> 175 <option value="custom">Custom</option>
176 <option value="ann">ANN</option> 176 </param>
177 <option value="custom">Custom</option> 177 <when value="csq">
178 </param> 178 <param name="vcf_info_field" type="hidden" value="CSQ"/>
179 <when value="csq"> 179 </when>
180 <param name="vcf_info_field" type="hidden" value="CSQ"/> 180 <when value="ann">
181 </when> 181 <param name="vcf_info_field" type="hidden" value="ANN"/>
182 <when value="ann"> 182 </when>
183 <param name="vcf_info_field" type="hidden" value="ANN"/> 183 <when value="custom">
184 </when> 184 <param name="vcf_info_field" type="text" label="Enter custom INFO key"/>
185 <when value="custom"> 185 </when>
186 <param name="vcf_info_field" type="text" label="Enter custom INFO key"/> 186 </conditional>
187 </when> 187 <param argument="--terms" type="select" label="Type of consequence terms to output" help="The default used for terms is Sequence Ontology.">
188 </conditional> 188 <option value="SO" selected="true">Sequence Ontology (SO)</option>
189 189 <option value="display">Display version of SO</option>
190 <param argument="--terms" type="select" label="Type of consequence terms to output" help="The default used for terms is Sequence Ontology."> 190 <option value="NCBI">NCBI</option>
191 <option value="SO" selected="true">Sequence Ontology (SO)</option> 191 </param>
192 <option value="display">Display version of SO</option> 192 <conditional name="shift_var">
193 <option value="NCBI">NCBI</option> 193 <param name="shift_selector" type="select" label="Shift variants to the right">
194 </param> 194 <option value="" selected="true">No shift</option>
195 195 <option value="--shift_hgvs 1">3' shift of HGVS notations, causing ambiguous insertions or deletions (typically in repetetive sequence tracts) to be "shifted" to their most 3' possible coordinates (relative to the transcript sequence and strand) before the HGVS notations are calculated (--shift_hgvs 1)</option>
196 <conditional name="shift_var"> 196 <option value="--shift_hgvs 0 --shift_3prime 1">Right align all variants relative to their associated transcripts prior to consequence calculation (--shift_3prime 1)</option>
197 <param name="shift_selector" type="select" label="Shift variants to the right"> 197 <option value="--shift_hgvs 0 --shift_genomic 1">Right align all variants, including intergenic variants, before consequence calculation and update the Location field (--shift_genomic 1)</option>
198 <option value="" selected="true">No shift</option> 198 </param>
199 <option value="--shift_hgvs 1">3' shift of HGVS notations, causing ambiguous insertions or deletions (typically in repetetive sequence tracts) to be "shifted" to their most 3' possible coordinates (relative to the transcript sequence and strand) before the HGVS notations are calculated (--shift_hgvs 1)</option> 199 <when value="" />
200 <option value="--shift_hgvs 0 --shift_3prime 1">Right align all variants relative to their associated transcripts prior to consequence calculation (--shift_3prime 1)</option> 200 <when value="--shift_hgvs 1" />
201 <option value="--shift_hgvs 0 --shift_genomic 1">Right align all variants, including intergenic variants, before consequence calculation and update the Location field (--shift_genomic 1)</option> 201 <when value="--shift_hgvs 0 --shift_3prime 1">
202 </param> 202 <param name="shift_length" type="boolean" truevalue="--shift_length" falsevalue="" label="Report the distance each variant has been shifted"/>
203 <when value=""/> 203 </when>
204 <when value="--shift_hgvs 1"/> 204 <when value="--shift_hgvs 0 --shift_genomic 1" />
205 <when value="--shift_hgvs 0 --shift_3prime 1"> 205 </conditional>
206 <param name="shift_length" type="boolean" truevalue="--shift_length" falsevalue="" label="Report the distance each variant has been shifted"/> 206 <param name="out_opt_checkboxes" type="select" optional="true" display="checkboxes" multiple="true" label="Output option flags">
207 </when> 207 <option value="--variant_class">Ouput variant class (--variant_class)</option>
208 <when value="--shift_hgvs 0 --shift_genomic 1"/> 208 <option value="--humdiv">Retrieve humDiv PolyPhen prediction instead of humVar (--humdiv)</option>
209 </conditional> 209 <option value="--overlaps">Output overlap between transcript and structural variant (--overlaps)</option>
210 210 <option value="--gene_phenotype">Indicate if the overlapped gene is associated with a phenotype, disease or trait (--gene_phenotype)</option>
211 <param name="out_opt_checkboxes" type="select" optional="true" display="checkboxes" multiple="true" label="Output option flags"> 211 <option value="--regulatory">Look for overlaps with regulatory regions (--regulatory)</option>
212 <option value="--variant_class">Ouput variant class (--variant_class)</option> 212 <option value="--phased">Force VCF genotypes to be interpreted as phased (--phased)</option>
213 <option value="--humdiv">Retrieve humDiv PolyPhen prediction instead of humVar (--humdiv)</option> 213 <option value="--allele_number">Identify allele number from VCF input, where 1 = first ALT allele etc. (--allele_number)</option>
214 <option value="--overlaps">Output overlap between transcript and structural variant (--overlaps)</option> 214 <option value="--show_ref_allele">Adds the reference allele in the output (--show_ref_allele)</option>
215 <option value="--gene_phenotype">Indicate if the overlapped gene is associated with a phenotype, disease or trait (--gene_phenotype)</option> 215 <option value="--total_length">Give cDNA, CDS and protein positions as Position/Length (--total_length)</option>
216 <option value="--regulatory">Look for overlaps with regulatory regions (--regulatory)</option> 216 <option value="--numbers">Output affected exon and intron numbering (--numbers)</option>
217 <option value="--phased">Force VCF genotypes to be interpreted as phased (--phased)</option> 217 <option value="--no_escape">Don't URI escape HGVS strings (--no_escape)</option>
218 <option value="--allele_number">Identify allele number from VCF input, where 1 = first ALT allele etc. (--allele_number)</option> 218 <option value="--keep_csq">Don't overwrite existing CSQ entry in VCF INFO field (--keep_csq)</option>
219 <option value="--show_ref_allele">Adds the reference allele in the output (--show_ref_allele)</option> 219 <option value="--no_headers">Don't write header lines in output files (--no_headers)</option>
220 <option value="--total_length">Give cDNA, CDS and protein positions as Position/Length (--total_length)</option> 220 </param>
221 <option value="--numbers">Output affected exon and intron numbering (--numbers)</option> 221 </section>
222 <option value="--no_escape">Don't URI escape HGVS strings (--no_escape)</option> 222 <section name="ident" title="Identifiers">
223 <option value="--keep_csq">Don't overwrite existing CSQ entry in VCF INFO field (--keep_csq)</option> 223 <param type="data" optional="true" name="input_synonyms" format="tabular" label="Load a file of chromosome synonyms" help="File should be tab-delimited with the primary identifier in column 1 and the synonym in column 2. Synonyms allow different chromosome identifiers to be used in the input file and any annotation source. (--synonyms [file])"/>
224 <option value="--no_headers">Don't write header lines in output files (--no_headers)</option> 224 <param name="ident_checkboxes" type="select" optional="true" display="checkboxes" multiple="true" label="Identifier flags">
225 </param> 225 <option value="--hgvs">Add HGVS nomenclature, both coding and protein sequence names, to the ouput (requires FASTA) (--hgvs)</option>
226 </section> 226 <option value="--hgvsg">Add genomic HGVS nomenclature based on the input chromosome name (requires FASTA) (--hgvsg)</option>
227 <section name="ident" title="Identifiers"> 227 <option value="--spdi">Add genomic SPDI notation (requires FASTA) (--spdi)</option>
228 <param type="data" optional="true" name="input_synonyms" format="tabular" label="Load a file of chromosome synonyms" help="File should be tab-delimited with the primary identifier in column 1 and the synonym in column 2. Synonyms allow different chromosome identifiers to be used in the input file and any annotation source. (--synonyms [file])"/> 228 <option value="--transcript_version">Add version numbers to Ensembl transcript identifiers (--transcript_version)</option>
229 <param name="ident_checkboxes" type="select" optional="true" display="checkboxes" multiple="true" label="Identifier flags"> 229 <option value="--protein">Add the Ensembl protein identifier to the output where appropriate (--protein)</option>
230 <option value="--hgvs">Add HGVS nomenclature, both coding and protein sequence names, to the ouput (requires FASTA) (--hgvs)</option> 230 <option value="--symbol">Add the gene symbol (e.g. HGNC) (where available) to the output (--symbol)</option>
231 <option value="--hgvsg">Add genomic HGVS nomenclature based on the input chromosome name (requires FASTA) (--hgvsg)</option> 231 <option value="--ccds">Add the CCDS transcript identifer (where available) to the output (--ccds)</option>
232 <option value="--spdi">Add genomic SPDI notation (requires FASTA) (--spdi)</option> 232 <option value="--uniprot">Add best match accessions for translated protein products from three UniProt-related databases (SWISSPROT, TREMBL and UniParc) to the output (--uniprot)</option>
233 <option value="--transcript_version">Add version numbers to Ensembl transcript identifiers (--transcript_version)</option> 233 <option value="--tsl">Add the transcript support level for this transcript to the output (only for hg38) (--tsl)</option>
234 <option value="--protein">Add the Ensembl protein identifier to the output where appropriate (--protein)</option> 234 <option value="--appris">Add the APPRIS isoform annotation for this transcript to the output (only for hg38) (--appris)</option>
235 <option value="--symbol">Add the gene symbol (e.g. HGNC) (where available) to the output (--symbol)</option> 235 <option value="--canonical">Add a flag indicating if the transcript is the canonical transcript for the gene (--canonical)</option>
236 <option value="--ccds">Add the CCDS transcript identifer (where available) to the output (--ccds)</option> 236 <option value="--mane">Add a flag indicating if the transcript is the MANE Select or MANE Plus Clinical transcript for the gene (only for hg38) (--mane)</option>
237 <option value="--uniprot">Add best match accessions for translated protein products from three UniProt-related databases (SWISSPROT, TREMBL and UniParc) to the output (--uniprot)</option> 237 <option value="--mane_select">Add a flag indicating if the transcript is the MANE Select transcript for the gene (only for hg38) (--mane_select)</option>
238 <option value="--tsl">Add the transcript support level for this transcript to the output (only for hg38) (--tsl)</option> 238 <option value="--biotype">Output the biotype of the transcript or regulatory feature (--biotype)</option>
239 <option value="--appris">Add the APPRIS isoform annotation for this transcript to the output (only for hg38) (--appris)</option> 239 <option value="--domains">Add names of overlapping protein domains to output (--domains)</option>
240 <option value="--canonical">Add a flag indicating if the transcript is the canonical transcript for the gene (--canonical)</option> 240 <option value="--xref_refseq">Output aligned RefSeq mRNA identifier for transcript (--xref_refseq)</option>
241 <option value="--mane">Add a flag indicating if the transcript is the MANE Select or MANE Plus Clinical transcript for the gene (only for hg38) (--mane)</option> 241 </param>
242 <option value="--mane_select">Add a flag indicating if the transcript is the MANE Select transcript for the gene (only for hg38) (--mane_select)</option> 242 </section>
243 <option value="--biotype">Output the biotype of the transcript or regulatory feature (--biotype)</option> 243 <section name="colo_var" title="Co-located variants">
244 <option value="--domains">Add names of overlapping protein domains to output (--domains)</option> 244 <param name="colo_var_checkboxes" type="select" optional="true" display="checkboxes" multiple="true" label="Co-located variants flags">
245 <option value="--xref_refseq">Output aligned RefSeq mRNA identifier for transcript (--xref_refseq)</option> 245 <option value="--check_existing">Check for the existence of known variants that are co-located with the input (--check_existing)</option>
246 </param> 246 <option value="--clin_sig_allele 0">Report all known clinical significance values at the given locus (instead of allele-specific) (--clin_sig_allele 0)</option>
247 </section> 247 <option value="--exclude_null_alleles">Do not include variants with unknown alleles when checking for co-located variants (--exclude_null_alleles)</option>
248 <section name="colo_var" title="Co-located variants"> 248 <option value="--no_check_alleles">When checking for existing variants, compare using coordinates only (--no_check_alleles)</option>
249 <param name="colo_var_checkboxes" type="select" optional="true" display="checkboxes" multiple="true" label="Co-located variants flags"> 249 <option value="--af">Add the global allele frequency (AF) from 1000 Genomes Phase 3 data for any known co-located variant to the output (--af)</option>
250 <option value="--check_existing">Check for the existence of known variants that are co-located with the input (--check_existing)</option> 250 <option value="--max_af">Report the highest allele frequency observed in any population from 1000 genomes, ESP or gnomAD (--max_af)</option>
251 <option value="--clin_sig_allele 0">Report all known clinical significance values at the given locus (instead of allele-specific) (--clin_sig_allele 0)</option> 251 <option value="--af_1kg">Add allele frequency from continental populations (AFR,AMR,EAS,EUR,SAS) of 1000 Genomes Phase 3 to the output (--af_1kg)</option>
252 <option value="--exclude_null_alleles">Do not include variants with unknown alleles when checking for co-located variants (--exclude_null_alleles)</option> 252 <option value="--af_esp">Include allele frequency from NHLBI-ESP populations (--af_esp)</option>
253 <option value="--no_check_alleles">When checking for existing variants, compare using coordinates only (--no_check_alleles)</option> 253 <option value="--af_gnomad">Include allele frequency from Genome Aggregation Database (gnomAD) exome populations (--af_gnomad)</option>
254 <option value="--af">Add the global allele frequency (AF) from 1000 Genomes Phase 3 data for any known co-located variant to the output (--af)</option> 254 <option value="--af_exac">Include allele frequency from ExAC project populations (--af_exac)</option>
255 <option value="--max_af">Report the highest allele frequency observed in any population from 1000 genomes, ESP or gnomAD (--max_af)</option> 255 <option value="--pubmed">Report Pubmed IDs for publications that cite existing variant (--pubmed)</option>
256 <option value="--af_1kg">Add allele frequency from continental populations (AFR,AMR,EAS,EUR,SAS) of 1000 Genomes Phase 3 to the output (--af_1kg)</option> 256 <option value="--var_synonyms">Report known synonyms for co-located variants (--var_synonyms)</option>
257 <option value="--af_esp">Include allele frequency from NHLBI-ESP populations (--af_esp)</option> 257 <option value="--failed 1">Do not exclude variants that have been flagged as failed when checking for co-located variants (--failed 1)</option>
258 <option value="--af_gnomad">Include allele frequency from Genome Aggregation Database (gnomAD) exome populations (--af_gnomad)</option> 258 </param>
259 <option value="--af_exac">Include allele frequency from ExAC project populations (--af_exac)</option> 259 </section>
260 <option value="--pubmed">Report Pubmed IDs for publications that cite existing variant (--pubmed)</option> 260 <section name="fil_qc" title="Filtering and QC options">
261 <option value="--var_synonyms">Report known synonyms for co-located variants (--var_synonyms)</option> 261 <param name="fil_qc_checkboxes" type="select" optional="true" display="checkboxes" multiple="true" label="Filtering and QC flags">
262 <option value="--failed 1">Do not exclude variants that have been flagged as failed when checking for co-located variants (--failed 1)</option> 262 <option value="--coding_only">Only return consequences that fall in the coding regions of transcripts (--coding_only)</option>
263 </param> 263 <option value="--no_intergenic">Do not include intergenic consequences in the output (--no_intergenic)</option>
264 </section> 264 </param>
265 <section name="fil_qc" title="Filtering and QC options"> 265 </section>
266 <param name="fil_qc_checkboxes" type="select" optional="true" display="checkboxes" multiple="true" label="Filtering and QC flags"> 266 <section name="plugins" title="VEP Plugins">
267 <option value="--coding_only">Only return consequences that fall in the coding regions of transcripts (--coding_only)</option> 267 <param name="carol" type="boolean" label="Enable Carol plugin" truevalue="--plugin Carol" falsevalue="" help="This plugin calculates the Combined Annotation scoRing toOL (CAROL) score for a missense mutation and adds it to VEP's output. Both the SIFT and PolyPhen-2 scores are required for the calculation, so these two have to be activated in the output options section." />
268 <option value="--no_intergenic">Do not include intergenic consequences in the output (--no_intergenic)</option> 268 <param name="condel" type="boolean" label="Enable Condel plugin" truevalue="--plugin Condel" falsevalue="" help="This plugin calculates the Consensus Deleteriousness (Condel) score for a missense mutation and adds it to VEP's output. Both the SIFT and PolyPhen-2 scores are required for the calculation, so these two have to be activated in the output options section." />
269 </param> 269 <param name="exacpli_file" type="data" format="txt" optional="true" label="Enable ExACpLI plugin by selecting an ExACpLI_values text file" help="This plugin calculates the probabililty of a gene being loss-of-function intolerant (pLI) and adds it to VEP's output. The closer pLI is to 1, the more likely the gene is loss-of-function (LoF) intolerant. An ExACpLI_values.txt file is required for usage and it is recommended to use the one provided in the VEP_plugins GitHub repository: https://github.com/Ensembl/VEP_plugins" />
270 </section> 270 <param name="loftool_file" type="data" format="txt" optional="true" label="Enable LoFtool plugin by selecting a LoFtool_scores text file" help="This plugin calculates LoFtool scores and adds them to VEP's output. LoFtool provides a rank of genic intolerance and consequent susceptibility to disease based on the ratio of Loss-of-function (LoF) to synonymous mutations for each gene in 60,706 individuals from ExAC, adjusting for the gene de novo mutation rate and evolutionary protein conservation. The lower the LoFtool gene score percentile the most intolerant is the gene to functional variation. A LoFtool_scores.txt file is required for usage and it is recommended to use the one provided in the VEP_plugins GitHub repository: https://github.com/Ensembl/VEP_plugins" />
271 <section name="plugins" title="VEP Plugins"> 271 </section>
272 <param name="carol" type="boolean" label="Enable Carol plugin" truevalue="--plugin Carol" falsevalue="" help="This plugin calculates the Combined Annotation scoRing toOL (CAROL) score for a missense mutation and adds it to VEP's output. Both the SIFT and PolyPhen-2 scores are required for the calculation, so these two have to be activated in the output options section." /> 272 </inputs>
273 <param name="condel" type="boolean" label="Enable Condel plugin" truevalue="--plugin Condel" falsevalue="" help="This plugin calculates the Consensus Deleteriousness (Condel) score for a missense mutation and adds it to VEP's output. Both the SIFT and PolyPhen-2 scores are required for the calculation, so these two have to be activated in the output options section." /> 273 <outputs>
274 <param name="exacpli_file" type="data" format="txt" optional="true" label="Enable ExACpLI plugin by selecting an ExACpLI_values text file" help="This plugin calculates the probabililty of a gene being loss-of-function intolerant (pLI) and adds it to VEP's output. The closer pLI is to 1, the more likely the gene is loss-of-function (LoF) intolerant. An ExACpLI_values.txt file is required for usage and it is recommended to use the one provided in the VEP_plugins GitHub repository: https://github.com/Ensembl/VEP_plugins" /> 274 <data name="output1" format="vcf" from_work_dir="MainOutput.vcf" />
275 <param name="loftool_file" type="data" format="txt" optional="true" label="Enable LoFtool plugin by selecting a LoFtool_scores text file" help="This plugin calculates LoFtool scores and adds them to VEP's output. LoFtool provides a rank of genic intolerance and consequent susceptibility to disease based on the ratio of Loss-of-function (LoF) to synonymous mutations for each gene in 60,706 individuals from ExAC, adjusting for the gene de novo mutation rate and evolutionary protein conservation. The lower the LoFtool gene score percentile the most intolerant is the gene to functional variation. A LoFtool_scores.txt file is required for usage and it is recommended to use the one provided in the VEP_plugins GitHub repository: https://github.com/Ensembl/VEP_plugins" /> 275 <data name="output2" format="txt" label="${tool.name} on ${on_string} TXT Summary" from_work_dir="MainOutput.vcf_summary.txt" />
276 </section> 276 </outputs>
277 </inputs> 277 <tests>
278 <outputs> 278 <!-- Note: need to use source: unrestricted in all tests involving a
279 <data name="output1" format="vcf" from_work_dir="MainOutput.vcf" /> 279 cache_file to be able to use outdated test caches with their version no
280 <data name="output2" format="txt" label="${tool.name} on ${on_string} TXT Summary" from_work_dir="MainOutput.vcf_summary.txt" /> 280 longer matching the tool version.
281 </outputs> 281 The alternative would be to update the cache file with every new tool
282 <tests> 282 release.
283 <test expect_num_outputs="2"> 283 Also note: VEP VCF outputs will feature two irreproducible header lines
284 <param name="source" value="restricted" /> 284 with run time info, which are dropped from the test files.
285 <param name="input1" dbkey="dm6" value="input_test1.vcf" ftype="vcf" /> 285 => always expect a two lines diff -->
286 <param name="cache_file" value="drosophila_melanogaster_vep_106_BDGP6.32" /> 286 <test expect_num_outputs="2">
287 <output name="output1" file="output_test1.vcf" ftype="vcf" lines_diff="2" /> 287 <param name="source" value="unrestricted" />
288 </test> 288 <param name="input1" dbkey="dm6" value="input_test1.vcf" ftype="vcf" />
289 <test expect_num_outputs="2"> 289 <param name="cache_file" value="drosophila_melanogaster_vep_106_BDGP6.32" />
290 <param name="source" value="custom" /> 290 <output name="output1" file="output_test1.vcf" ftype="vcf" lines_diff="2" />
291 <param name="input1" dbkey="hg19" value="input_test2.vcf" ftype="vcf" /> 291 </test>
292 <param name="custom_annotation" dbkey="hg19" value="test.gtf" ftype="gtf" /> 292 <test expect_num_outputs="2">
293 <param name="ref_source" value="history" /> 293 <param name="source" value="custom" />
294 <param name="ref" dbkey="hg19" value="test.fa" ftype="fasta" /> 294 <param name="input1" dbkey="hg19" value="input_test2.vcf" ftype="vcf" />
295 <output name="output1" file="output_test2.vcf" ftype="vcf" lines_diff="2" /> 295 <param name="custom_annotation" dbkey="hg19" value="test.gtf" ftype="gtf" />
296 </test> 296 <param name="ref_source" value="history" />
297 <test expect_num_outputs="2"> 297 <param name="ref" dbkey="hg19" value="test.fa" ftype="fasta" />
298 <param name="source" value="restricted" /> 298 <output name="output1" file="output_test2.vcf" ftype="vcf" lines_diff="2" />
299 <param name="input1" dbkey="dm6" value="input_test1.vcf" ftype="vcf" /> 299 </test>
300 <param name="cache_file" value="drosophila_melanogaster_vep_106_BDGP6.32" /> 300 <test expect_num_outputs="2">
301 <param name="source" value="restricted" /> 301 <param name="source" value="unrestricted" />
302 <param name="vcf_info_field" value="ANN" /> 302 <param name="input1" dbkey="dm6" value="input_test1.vcf" ftype="vcf" />
303 <output name="output1"> 303 <param name="cache_file" value="drosophila_melanogaster_vep_106_BDGP6.32" />
304 <assert_contents> 304 <param name="vcf_info_field" value="ANN" />
305 <has_text text="##INFO=&lt;ID=ANN" /> 305 <output name="output1">
306 <has_n_lines n="5" /> 306 <assert_contents>
307 </assert_contents> 307 <has_text text="##INFO=&lt;ID=ANN" />
308 </output> 308 <has_n_lines n="6" />
309 </test> 309 </assert_contents>
310 <test expect_num_outputs="2"> 310 </output>
311 <param name="source" value="restricted" /> 311 </test>
312 <param name="input1" dbkey="dm6" value="input_test1.vcf" ftype="vcf" /> 312 <test expect_num_outputs="2">
313 <param name="cache_file" value="drosophila_melanogaster_vep_106_BDGP6.32" /> 313 <param name="source" value="unrestricted" />
314 <param name="source" value="restricted" /> 314 <param name="input1" dbkey="dm6" value="input_test1.vcf" ftype="vcf" />
315 <param name="terms" value="display" /> 315 <param name="cache_file" value="drosophila_melanogaster_vep_106_BDGP6.32" />
316 <output name="output1"> 316 <param name="terms" value="display" />
317 <assert_contents> 317 <output name="output1">
318 <has_text text="|DOWNSTREAM|" /> 318 <assert_contents>
319 <not_has_text text="|downstream_gene_variant|" /> 319 <has_text text="|DOWNSTREAM|" />
320 <has_text text="|UPSTREAM|" /> 320 <not_has_text text="|downstream_gene_variant|" />
321 <not_has_text text="|upstream_gene_variant|" /> 321 <has_text text="|UPSTREAM|" />
322 <has_n_lines n="5" /> 322 <not_has_text text="|upstream_gene_variant|" />
323 </assert_contents> 323 <has_n_lines n="6" />
324 </output> 324 </assert_contents>
325 </test> 325 </output>
326 <test expect_num_outputs="2"> 326 </test>
327 <param name="source" value="restricted" /> 327 <test expect_num_outputs="2">
328 <param name="input1" dbkey="dm6" value="input_test1.vcf" ftype="vcf" /> 328 <param name="source" value="unrestricted" />
329 <param name="cache_file" value="drosophila_melanogaster_vep_106_BDGP6.32" /> 329 <param name="input1" dbkey="dm6" value="input_test1.vcf" ftype="vcf" />
330 <param name="source" value="restricted" /> 330 <param name="cache_file" value="drosophila_melanogaster_vep_106_BDGP6.32" />
331 <param name="out_opt_checkboxes" value="--overlaps,--allele_number" /> 331 <param name="out_opt_checkboxes" value="--overlaps,--allele_number" />
332 <output name="output1"> 332 <output name="output1">
333 <assert_contents> 333 <assert_contents>
334 <has_text text="|OverlapBP|OverlapPC" /> 334 <has_text text="|OverlapBP|OverlapPC" />
335 <has_text text="|ALLELE_NUM" /> 335 <has_text text="|ALLELE_NUM" />
336 <has_n_lines n="5" /> 336 <has_n_lines n="6" />
337 </assert_contents> 337 </assert_contents>
338 </output> 338 </output>
339 </test> 339 </test>
340 <test expect_num_outputs="2"> 340 <test expect_num_outputs="2">
341 <param name="source" value="restricted" /> 341 <param name="source" value="unrestricted" />
342 <param name="input1" dbkey="dm6" value="input_test1.vcf" ftype="vcf" /> 342 <param name="input1" dbkey="dm6" value="input_test1.vcf" ftype="vcf" />
343 <param name="cache_file" value="drosophila_melanogaster_vep_106_BDGP6.32" /> 343 <param name="cache_file" value="drosophila_melanogaster_vep_106_BDGP6.32" />
344 <param name="source" value="restricted" /> 344 <param name="ident_checkboxes" value="--uniprot,--biotype" />
345 <param name="ident_checkboxes" value="--uniprot,--biotype" /> 345 <output name="output1">
346 <output name="output1"> 346 <assert_contents>
347 <assert_contents> 347 <has_text text="|SWISSPROT|TREMBL|UNIPARC|UNIPROT_ISOFORM" />
348 <has_text text="|SWISSPROT|TREMBL|UNIPARC|UNIPROT_ISOFORM" /> 348 <has_text text="|BIOTYPE" />
349 <has_text text="|BIOTYPE" /> 349 <has_n_lines n="6" />
350 <has_n_lines n="5" /> 350 </assert_contents>
351 </assert_contents> 351 </output>
352 </output> 352 </test>
353 </test> 353 <test expect_num_outputs="2">
354 <test expect_num_outputs="2"> 354 <param name="source" value="unrestricted" />
355 <param name="source" value="restricted" /> 355 <param name="input1" dbkey="dm6" value="input_test1.vcf" ftype="vcf" />
356 <param name="input1" dbkey="dm6" value="input_test1.vcf" ftype="vcf" /> 356 <param name="cache_file" value="drosophila_melanogaster_vep_106_BDGP6.32" />
357 <param name="cache_file" value="drosophila_melanogaster_vep_106_BDGP6.32" /> 357 <param name="colo_var_checkboxes" value="--max_af,--pubmed" />
358 <param name="source" value="restricted" /> 358 <output name="output1">
359 <param name="colo_var_checkboxes" value="--max_af,--pubmed" /> 359 <assert_contents>
360 <output name="output1"> 360 <has_text text="|MAX_AF|MAX_AF_POPS" />
361 <assert_contents> 361 <has_text text="|PUBMED" />
362 <has_text text="|MAX_AF|MAX_AF_POPS" /> 362 <has_n_lines n="6" />
363 <has_text text="|PUBMED" /> 363 </assert_contents>
364 <has_n_lines n="5" /> 364 </output>
365 </assert_contents> 365 </test>
366 </output> 366 </tests>
367 </test> 367 <help><![CDATA[
368 </tests> 368 The Ensembl Variant Effect Predictor (VEP) is able to determine the effect of variants (e.g. SNPs, insertions or deletions) on genes, transcripts, protein sequences and regulatory regions. Given the coordinates and nucleotide changes of a variant, it outputs affected genes, the exact location and consequences of the variant as well as known variants matching this one.
369 <help><![CDATA[ 369 ]]></help>
370 The Ensembl Variant Effect Predictor (VEP) is able to determine the effect of variants (e.g. SNPs, insertions or deletions) on genes, transcripts, protein sequences and regulatory regions. Given the coordinates and nucleotide changes of a variant, it outputs affected genes, the exact location and consequences of the variant as well as known variants matching this one. 370 <citations>
371 ]]></help> 371 <citation type="doi">10.1186/s13059-016-0974-4</citation>
372 <citations> 372 </citations>
373 <citation type="doi">10.1186/s13059-016-0974-4</citation>
374 </citations>
375 </tool> 373 </tool>