snpeff: snpEff.xml annotate

annotate snpEff.xml @ 29:ca2b512e8d7c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7

author	iuc
date	Mon, 21 Oct 2024 13:56:15 +0000
parents	6322be79bd8e
children

rev	line source
29 ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	1 <tool id="snpEff" name="SnpEff eff:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0">
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	2 <description> annotate variants</description>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	3 <macros>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	4 <import>snpEff_macros.xml</import>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	5 </macros>
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	6 <requirements>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	7 <expand macro="requirement" />
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	8 </requirements>
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	9 <expand macro="stdio" />
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	10 <expand macro="version_command" />
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	11 <command><![CDATA[
26 5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	12 #if $intervals
5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	13 ln -s '${intervals}' intervals.bed &&
5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	14 #end if
17 65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 14 diff changeset	15 snpEff @JAVA_OPTIONS@ eff
29 ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	16 -i $inputFormat -o ${outputFormat} -upDownStreamLen $udLength
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	17 #if $spliceSiteSize and str($spliceSiteSize) != '':
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	18 -spliceSiteSize "$spliceSiteSize"
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	19 #end if
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	20 #if $spliceRegion.setSpliceRegions == 'yes':
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	21 #if str($spliceRegion.spliceRegionExonSize)
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	22 -spliceRegionExonSize $spliceRegion.spliceRegionExonSize
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	23 #end if
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	24 #if str($spliceRegion.spliceRegionIntronMin)
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	25 -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	26 #end if
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	27 #if str($spliceRegion.spliceRegionIntronMax)
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	28 -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	29 #end if
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	30 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	31 #if $annotations and str($annotations) != '':
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	32 #echo " "
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	33 #echo ' '.join(str($annotations).split(','))
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	34 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	35 #if $filterOut and str($filterOut) != '':
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	36 #echo " "
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	37 #echo ' '.join(str($filterOut).split(','))
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	38 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	39 #if $filter.specificEffects == 'yes' and $filter.effects:
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	40 #for $eff in str($filter.effects).split(','):
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	41 -no $eff
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	42 #end for
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	43 #end if
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	44 #if $transcripts
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	45 -onlyTr '$transcripts'
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	46 #end if
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	47 #if $intervals ### fix this for multiple dataset input
26 5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	48 -interval intervals.bed
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	49 #end if
e8adfc4c0a6b Uploaded iuc parents: diff changeset	50 #if $statsFile:
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	51 -stats '$statsFile'
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	52 #end if
14 85ca751407c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 12 diff changeset	53 #if $csvStats:
85ca751407c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 12 diff changeset	54 -csvStats '$csvFile'
85ca751407c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 12 diff changeset	55 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	56 #if str($chr).strip() != '':
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	57 -chr '$chr'
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	58 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	59 $noLog
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	60 ## Regulation names can include parentheses: H3K4me3-MSC_(VB)_enriched_sites
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	61 ## Enclose them in in single and double quotes, as the conda snpEff bash script will remove outer quotes
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	62 #if $snpDb.genomeSrc == 'cached':
e8adfc4c0a6b Uploaded iuc parents: diff changeset	63 -dataDir ${snpDb.genomeVersion.fields.path}
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	64 #if $snpDb.reg_section.regulation and str($snpDb.reg_section.regulation) != '':
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	65 #set $regs = [x for x in str($snpDb.reg_section.regulation).split(',')]
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	66 #for reg in $regs:
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	67 -reg '"${reg}"'
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	68 #end for
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	69 #end if
e8adfc4c0a6b Uploaded iuc parents: diff changeset	70 $snpDb.genomeVersion
e8adfc4c0a6b Uploaded iuc parents: diff changeset	71 #elif $snpDb.genomeSrc == 'history':
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	72 -dataDir '${snpDb.snpeff_db.extra_files_path}'
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	73 #if $snpDb.reg_section.regulation and str($snpDb.reg_section.regulation) != '':
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	74 #set $regs = [x for x in str($snpDb.reg_section.regulation).split(',')]
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	75 #for reg in $regs:
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	76 -reg '"${reg}"'
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	77 #end for
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	78 #end if
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	79 '${snpDb.snpeff_db.metadata.genome_version}'
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	80 #elif $snpDb.genomeSrc == 'custom':
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	81 -dataDir '${snpDb.snpeff_db.extra_files_path}'
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	82 -configOption '${snpDb.snpeff_db.metadata.genome_version}'.genome='${snpDb.snpeff_db.metadata.genome_version}'
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	83 -configOption '${snpDb.snpeff_db.metadata.genome_version}'.codonTable='${snpDb.codon_table}'
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	84 '${snpDb.snpeff_db.metadata.genome_version}'
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	85 #else
20 8f92c2b26e6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa iuc parents: 17 diff changeset	86 -dataDir "\$PWD/temp"
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	87 -download
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	88 '$snpDb.genome_version'
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	89 #end if
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	90 '$input' > '$snpeff_output'
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	91 #if $statsFile:
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	92 &&
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	93 #import os
14 85ca751407c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 12 diff changeset	94 #if $csvStats:
85ca751407c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 12 diff changeset	95 #set $genes_file = str($csvFile) + '.genes.txt'
85ca751407c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 12 diff changeset	96 #else
85ca751407c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 12 diff changeset	97 #set $genes_file = str($statsFile) + '.genes.txt'
85ca751407c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 12 diff changeset	98 #end if
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	99 #set $genes_file_name = os.path.split($genes_file)[-1]
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	100 mkdir '$statsFile.files_path' &&
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	101 mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#'
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	102 #end if
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	103 ]]></command>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	104 <inputs>
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	105 <param name="input" type="data" format="vcf,bed" label="Sequence changes (SNPs, MNPs, InDels)"/>
29 ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	106 <param argument="-i" name="inputFormat" type="select" label="Input format" help="Specify the format of input dataset(s)">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	107 <option value="vcf" selected="true">VCF</option>
29 ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	108 <option value="bed">BED</option>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	109 </param>
29 ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	110 <param argument="-o" name="outputFormat" type="select" label="Output format" help="Specify output format">
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	111 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	112 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	113 <option value="bed">BED</option>
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	114 <option value="bedAnn">BED annotations</option>
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	115 </param>
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	116 <param argument="-csvStats" type="boolean" truevalue="-csvStats" falsevalue="" checked="false" label="Create CSV report?" help="Useful for downstream analyses and report generation" />
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	117 <param argument="-noStats" name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats?" help="Generates an HTML summary of results"/>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	118 <conditional name="snpDb">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	119 <param name="genomeSrc" type="select" label="Genome source">
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	120 <!-- These options are referenced in the help section of SnpEff download tool. If you change them, change help of SnpEff download as well -->
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	121 <option value="cached">Locally installed snpEff database</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	122 <option value="history">Downloaded snpEff database in your history</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	123 <option value="named">Download on demand</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	124 <option value="custom">Custom snpEff database in your history</option>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	125 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	126 <when value="cached">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	127 <param name="genomeVersion" type="select" label="Genome">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	128 <!--GENOME DESCRIPTION-->
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	129 <options from_data_table="snpeffv_genomedb">
17 65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 14 diff changeset	130 <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/>
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	131 <filter type="unique_value" column="2" />
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	132 </options>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	133 </param>
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	134 <section name="reg_section" expanded="false" title="Regulation options">
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	135 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes">
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	136 <options from_data_table="snpeffv_regulationdb">
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	137 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	138 <filter type="unique_value" column="3" />
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	139 </options>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	140 </param>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	141 </section>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	142 </when>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	143 <when value="history">
17 65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 14 diff changeset	144 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 14 diff changeset	145 <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	146 </param>
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	147 <section name="reg_section" expanded="false" title="Regulation options">
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	148 <!-- From metadata -->
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	149 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes">
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	150 <options>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	151 <filter type="data_meta" ref="snpeff_db" key="regulation" />
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	152 </options>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	153 </param>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	154 </section>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	155 </when>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	156 <when value="named">
29 ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	157 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)" help="A list of databases can be obtained with 'snpEff download' tool">
17 65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 14 diff changeset	158 <validator type="empty_field" message="A genome version name is required" />
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	159 </param>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	160 </when>
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	161 <when value="custom">
17 65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 14 diff changeset	162 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 14 diff changeset	163 <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	164 </param>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	165 <param name="codon_table" type="select" label="Select genetic code for this sequence" help="If this sequence uses non-standard genetic code, select one from these options">
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	166 <option selected="true" value="Standard">Standard</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	167 <option value="Vertebrate_Mitochondrial">Vertebrate_Mitochondrial</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	168 <option value="Yeast_Mitochondrial">Yeast_Mitochondrial</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	169 <option value="Mold_Mitochondrial">Mold_Mitochondrial</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	170 <option value="Protozoan_Mitochondrial">Protozoan_Mitochondrial</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	171 <option value="Coelenterate">Coelenterate</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	172 <option value="Mitochondrial">Mitochondrial</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	173 <option value="Mycoplasma">Mycoplasma</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	174 <option value="Spiroplasma">Spiroplasma</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	175 <option value="Invertebrate_Mitochondrial">Invertebrate_Mitochondrial</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	176 <option value="Ciliate_Nuclear">Ciliate_Nuclear</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	177 <option value="Dasycladacean_Nuclear">Dasycladacean_Nuclear</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	178 <option value="Hexamita_Nuclear">Hexamita_Nuclear</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	179 <option value="Echinoderm_Mitochondrial">Echinoderm_Mitochondrial</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	180 <option value="Flatworm_Mitochondrial">Flatworm_Mitochondrial</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	181 <option value="Euplotid_Nuclear">Euplotid_Nuclear</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	182 <option value="Bacterial_and_Plant_Plastid">Bacterial_and_Plant_Plastid</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	183 <option value="Alternative_Yeast_Nuclear">Alternative_Yeast_Nuclear</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	184 <option value="Ascidian_Mitochondrial">Ascidian_Mitochondrial</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	185 <option value="Alternative_Flatworm_Mitochondrial">Alternative_Flatworm_Mitochondrial</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	186 <option value="Blepharisma_Macronuclear">Blepharisma_Macronuclear</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	187 <option value="Chlorophycean_Mitochondrial">Chlorophycean_Mitochondrial</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	188 <option value="Trematode_Mitochondrial">Trematode_Mitochondrial</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	189 <option value="Scenedesmus_obliquus_Mitochondrial">Scenedesmus_obliquus_Mitochondrial</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	190 <option value="Thraustochytrium_Mitochondrial">Thraustochytrium_Mitochondrial</option>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	191 </param>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	192 </when>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	193 </conditional>
17 65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 14 diff changeset	194 <param name="udLength" argument="-ud" type="select" label="Upstream / Downstream length">
29 ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	195 <option value="0" selected="true">No upstream / downstream intervals (0 bases)</option>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	196 <option value="200">200 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	197 <option value="500">500 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	198 <option value="1000">1000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	199 <option value="2000">2000 bases</option>
29 ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	200 <option value="5000">5000 bases</option>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	201 <option value="10000">10000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	202 <option value="20000">20000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	203 </param>
17 65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 14 diff changeset	204 <param name="spliceSiteSize" argument="-ss" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	205 <option value="1">1 base</option>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	206 <option value="2" selected="true">2 bases</option>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	207 <option value="3">3 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	208 <option value="4">4 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	209 <option value="5">5 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	210 <option value="6">6 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	211 <option value="7">7 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	212 <option value="8">8 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	213 <option value="9">9 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	214 </param>
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	215 <conditional name="spliceRegion">
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	216 <param name="setSpliceRegions" type="select" label="spliceRegion Settings">
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	217 <option value="no">Use Defaults</option>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	218 <option value="yes">Set Splice Region Parameters</option>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	219 </param>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	220 <when value="no"/>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	221 <when value="yes">
17 65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 14 diff changeset	222 <param argument="-spliceRegionExonSize" type="integer" value="" min="1" max="10" optional="true" label="Set size for splice site region within exons. Default: 3 bases" />
65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 14 diff changeset	223 <param argument="-spliceRegionIntronMin" type="integer" value="" min="1" max="10" optional="true" label="Set minimum number of bases for splice site region within intron. Default: 3 bases" />
65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 14 diff changeset	224 <param argument="-spliceRegionIntronMax" type="integer" value="" min="1" max="10" optional="true" label="Set maximum number of bases for splice site region within intron. Default: 8 bases" />
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	225 </when>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	226 </conditional>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	227 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	228 <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN')</option>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	229 <option value="-classic">Use Classic Effect names and amino acid variant annotations (NON_SYNONYMOUS_CODING vs missense_variant and G180R vs p.Gly180Arg/c.538G>C)</option>
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	230 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	231 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option>
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	232 <option value="-hgvsOld">Old notation style notation: E.g. 'c.G123T' instead of 'c.123G>T' and 'X' instead of '*'</option>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	233 <option value="-hgvs1LetterAa">Use one letter Amino acid codes in HGVS notation. E.g. p.R47G instead of p.Arg47Gly</option>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	234 <option value="-hgvsTrId">Use transcript ID in HGVS notation. E.g. ENST00000252100:c.914C>G instead of c.914C>G</option>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	235 <option value="-noShiftHgvs">Do not shift variants according to HGVS notation (most 3prime end)</option>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	236 <option value="-noHgvs">Do not add HGVS annotations</option>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	237 <option value="-canon">Only use canonical transcripts</option>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	238 <option value="-onlyProtein">Only use protein coding transcripts</option>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	239 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	240 <option value="-noExpandIUB">Disable IUB code expansion in input variants</option>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	241 <option value="-oicr">Add OICR tag in VCF file</option>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	242 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	243 <option value="-noLof">Do not add LOF and NMD annotations</option>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	244 <option value="-noMotif">Disable motif annotations</option>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	245 <option value="-noNextProt">Disable NextProt annotations</option>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	246 <option value="-noInteraction">Disable interaction annotations</option>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	247 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
8 ce135864629c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 9d2052269bfbca81a5f9cd10c3153e611358a329 iuc parents: 7 diff changeset	248 <!-- onlyReg option results in frequent exceptions with version 4.3k
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	249 <option value="-onlyReg">Only use regulation tracks</option>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	250 -->
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	251 </param>
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	252 <!-- -cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples. -->
17 65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 14 diff changeset	253 <param name="intervals" argument="-interval" type="data" format="bed" optional="true" label="Use custom interval file for annotation" />
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	254 <param name="transcripts" type="data" format="tabular" optional="true" label="Only use the transcripts in this file" help="Format is one transcript ID per line"/>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	255 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	256 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	257 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	258 <option value="-no-intron">Do not show INTRON changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	259 <option value="-no-upstream">Do not show UPSTREAM changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	260 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	261 </param>
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	262 <conditional name="filter">
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	263 <param name="specificEffects" type="select" label="Filter out specific Effects">
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	264 <option value="no">No</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	265 <option value="yes">Yes</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	266 </param>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	267 <when value="no"/>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	268 <when value="yes">
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	269 <param name="effects" type="select" display="checkboxes" multiple="true" label="Filter output: do not report these Effects">
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	270 <option value="CDS">CDS (coding_sequence_variant) The variant hits a CDS. MODIFIER</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	271 <option value="CHROMOSOME_LARGE_DELETION">CHROMOSOME_LARGE_DELETION (chromosome) A large parte (over 1%) of the chromosome was deleted. HIGH</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	272 <option value="CODON_CHANGE">CODON_CHANGE (coding_sequence_variant) One or many codons are changed e.g.: An MNP of size multiple of 3 MODERATE</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	273 <option value="CODON_INSERTION">CODON_INSERTION (inframe_insertion) One or many codons are inserted e.g.: An insert multiple of three in a codon boundary MODERATE</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	274 <option value="CODON_CHANGE_PLUS_CODON_INSERTION">CODON_CHANGE_PLUS_CODON_INSERTION (disruptive_inframe_insertion) One codon is changed and one or many codons are inserted e.g.: An insert of size multiple of three, not at codon boundary MODERATE</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	275 <option value="CODON_DELETION">CODON_DELETION (inframe_deletion) One or many codons are deleted e.g.: A deletion multiple of three at codon boundary MODERATE</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	276 <option value="CODON_CHANGE_PLUS_CODON_DELETION">CODON_CHANGE_PLUS_CODON_DELETION (disruptive_inframe_deletion) One codon is changed and one or more codons are deleted e.g.: A deletion of size multiple of three, not at codon boundary MODERATE</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	277 <option value="DOWNSTREAM">DOWNSTREAM (downstream_gene_variant) Downstream of a gene (default length: 5K bases) MODIFIER</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	278 <option value="EXON">EXON (exon_variant) The variant hits an exon (from a non-coding transcript) or a retained intron. MODIFIER</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	279 <option value="EXON_DELETED">EXON_DELETED (exon_loss_variant) A deletion removes the whole exon. HIGH</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	280 <option value="FRAME_SHIFT">FRAME_SHIFT (frameshift_variant) Insertion or deletion causes a frame shift e.g.: An indel size is not multple of 3 HIGH</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	281 <option value="GENE">GENE (gene_variant) The variant hits a gene. MODIFIER</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	282 <option value="INTERGENIC">INTERGENIC (intergenic_region) The variant is in an intergenic region MODIFIER</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	283 <option value="INTERGENIC_CONSERVED">INTERGENIC_CONSERVED (conserved_intergenic_variant) The variant is in a highly conserved intergenic region MODIFIER</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	284 <option value="INTRAGENIC">INTRAGENIC (intragenic_variant) The variant hits a gene, but no transcripts within the gene MODIFIER</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	285 <option value="INTRON">INTRON (intron_variant) Variant hits and intron. Technically, hits no exon in the transcript. MODIFIER</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	286 <option value="INTRON_CONSERVED">INTRON_CONSERVED (conserved_intron_variant) The variant is in a highly conserved intronic region MODIFIER</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	287 <option value="MICRO_RNA">MICRO_RNA (miRNA) Variant affects an miRNA MODIFIER</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	288 <option value="NON_SYNONYMOUS_CODING">NON_SYNONYMOUS_CODING (missense_variant) Variant causes a codon that produces a different amino acid e.g.: Tgg/Cgg, W/R MODERATE</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	289 <option value="NON_SYNONYMOUS_START">NON_SYNONYMOUS_START (initiator_codon_variant) Variant causes start codon to be mutated into another start codon (the new codon produces a different AA). e.g.: Atg/Ctg, M/L (ATG and CTG can be START codons) LOW</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	290 <option value="NON_SYNONYMOUS_STOP">NON_SYNONYMOUS_STOP (stop_retained_variant) Variant causes stop codon to be mutated into another stop codon (the new codon produces a different AA). e.g.: Atg/Ctg, M/L (ATG and CTG can be START codons) LOW</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	291 <option value="RARE_AMINO_ACID">RARE_AMINO_ACID (rare_amino_acid_variant) The variant hits a rare amino acid thus is likely to produce protein loss of function HIGH</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	292 <option value="SPLICE_SITE_ACCEPTOR">SPLICE_SITE_ACCEPTOR (splice_acceptor_variant) The variant hits a splice acceptor site (defined as two bases before exon start, except for the first exon). HIGH</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	293 <option value="SPLICE_SITE_DONOR">SPLICE_SITE_DONOR (splice_donor_variant) The variant hits a Splice donor site (defined as two bases after coding exon end, except for the last exon). HIGH</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	294 <option value="SPLICE_SITE_REGION">SPLICE_SITE_REGION (splice_region_variant) A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. LOW</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	295 <option value="SPLICE_SITE_BRANCH">SPLICE_SITE_BRANCH (splice_region_variant) A varaint affective putative (Lariat) branch point, located in the intron. LOW</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	296 <option value="SPLICE_SITE_BRANCH_U12">SPLICE_SITE_BRANCH_U12 (splice_region_variant) A varaint affective putative (Lariat) branch point from U12 splicing machinery, located in the intron. MODERATE</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	297 <option value="STOP_LOST">STOP_LOST (stop_lost) Variant causes stop codon to be mutated into a non-stop codon e.g.: Tga/Cga, */R HIGH</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	298 <option value="START_GAINED">START_GAINED (5_prime_UTR_premature start_codon_gain_variant) A variant in 5'UTR region produces a three base sequence that can be a START codon. LOW</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	299 <option value="START_LOST">START_LOST (start_lost) Variant causes start codon to be mutated into a non-start codon. e.g.: aTg/aGg, M/R HIGH</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	300 <option value="STOP_GAINED">STOP_GAINED (stop_gained) Variant causes a STOP codon e.g.: Cag/Tag, Q/* HIGH</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	301 <option value="SYNONYMOUS_CODING">SYNONYMOUS_CODING (synonymous_variant) Variant causes a codon that produces the same amino acid e.g.: Ttg/Ctg, L/L LOW</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	302 <option value="SYNONYMOUS_START">SYNONYMOUS_START (start_retained) Variant causes start codon to be mutated into another start codon. e.g.: Ttg/Ctg, L/L (TTG and CTG can be START codons) LOW</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	303 <option value="SYNONYMOUS_STOP">SYNONYMOUS_STOP (stop_retained_variant) Variant causes stop codon to be mutated into another stop codon. e.g.: taA/taG, / LOW</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	304 <option value="TRANSCRIPT">TRANSCRIPT (transcript_variant) The variant hits a transcript. MODIFIER</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	305 <option value="REGULATION">REGULATION (regulatory_region_variant) The variant hits a known regulatory feature (non-coding). MODIFIER</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	306 <option value="UPSTREAM">UPSTREAM (upstream_gene_variant) Upstream of a gene (default length: 5K bases) MODIFIER</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	307 <option value="UTR_3_PRIME">UTR_3_PRIME (3_prime_UTR_variant) Variant hits 3'UTR region MODIFIER</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	308 <option value="UTR_3_DELETED">UTR_3_DELETED (3_prime_UTR_truncation + exon_loss) The variant deletes an exon which is in the 3'UTR of the transcript MODERATE</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	309 <option value="UTR_5_PRIME">UTR_5_PRIME (5_prime_UTR_variant) Variant hits 5'UTR region MODIFIER</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	310 <option value="UTR_5_DELETED">UTR_5_DELETED (5_prime_UTR_truncation + exon_loss_variant) The variant deletes an exon which is in the 5'UTR of the transcript MODERATE</option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	311 <option value="NEXT_PROT">NEXT_PROT (sequence_feature + exon_loss_variant) A 'NextProt' based annotation. Details are provided in the 'feature type' sub-field (ANN), or in the effect details (EFF). MODERATE </option>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	312 </param>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	313 </when>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	314 </conditional>
17 65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 14 diff changeset	315 <param argument="-chr" type="text" label="Text to prepend to chromosome name">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	316 <help>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	317 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	318 You can prepend any string you want to the chromosome name
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	319 </help>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	320 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	321 </param>
17 65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 14 diff changeset	322 <param argument="-noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server" />
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	323 </inputs>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	324 <outputs>
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	325 <data name="snpeff_output" format="vcf">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	326 <change_format>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	327 <when input="outputConditional.outputFormat" value="bed" format="bed" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	328 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	329 </change_format>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	330 </data>
14 85ca751407c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 12 diff changeset	331 <data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats">
28 6322be79bd8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 26 diff changeset	332 <filter>generate_stats</filter>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	333 </data>
14 85ca751407c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 12 diff changeset	334 <data name="csvFile" format="csv" label="${tool.name} on ${on_string} - CSV stats">
28 6322be79bd8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 26 diff changeset	335 <filter>csvStats</filter>
14 85ca751407c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 12 diff changeset	336 </data>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	337 </outputs>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	338 <tests>
28 6322be79bd8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 26 diff changeset	339 <test expect_num_outputs="2">
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	340 <param name="input" ftype="vcf" value="input.vcf"/>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	341 <param name="inputFormat" value="vcf"/>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	342 <param name="outputFormat" value="vcf"/>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	343 <param name="genomeSrc" value="named"/>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	344 <param name="genome_version" value="ebola_zaire"/>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	345 <param name="udLength" value="0"/>
28 6322be79bd8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 26 diff changeset	346 <param name="generate_stats" value="true"/>
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	347 <output name="snpeff_output">
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	348 <assert_contents>
29 ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	349 <has_text_matching expression="KJ660346.1\t572\t.*missense_variant" />
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	350 <has_text_matching expression="KJ660346.1\t1024\t.*synonymous_variant" />
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	351 </assert_contents>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	352 </output>
28 6322be79bd8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 26 diff changeset	353 <output name="statsFile">
6322be79bd8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 26 diff changeset	354 <assert_contents>
6322be79bd8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 26 diff changeset	355 <has_text text="<b>"/>
6322be79bd8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 26 diff changeset	356 </assert_contents>
6322be79bd8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 26 diff changeset	357 </output>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	358 </test>
26 5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	359 <!-- Test interval option-->
28 6322be79bd8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 26 diff changeset	360 <test expect_num_outputs="2">
26 5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	361 <param name="input" ftype="vcf" value="input.vcf"/>
5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	362 <param name="inputFormat" value="vcf"/>
5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	363 <param name="outputFormat" value="vcf"/>
5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	364 <param name="genomeSrc" value="named"/>
5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	365 <param name="interval" value="intervals.bed"/>
5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	366 <param name="genome_version" value="ebola_zaire"/>
5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	367 <param name="udLength" value="0"/>
5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	368 <param name="generate_stats" value="false"/>
28 6322be79bd8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 26 diff changeset	369 <param name="csvStats" value="true"/>
26 5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	370 <output name="snpeff_output">
5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	371 <assert_contents>
29 ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	372 <has_text_matching expression="KJ660346.1\t572\t.*missense_variant" />
ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	373 <has_text_matching expression="KJ660346.1\t1024\t.*synonymous_variant" />
26 5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	374 </assert_contents>
5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	375 </output>
28 6322be79bd8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 26 diff changeset	376 <output name="csvFile">
6322be79bd8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 26 diff changeset	377 <assert_contents>
29 ca2b512e8d7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 28 diff changeset	378 <has_n_lines n="134"/>
28 6322be79bd8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 26 diff changeset	379 <has_n_columns n="1" sep=","/>
6322be79bd8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 26 diff changeset	380 </assert_contents>
6322be79bd8e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 26 diff changeset	381 </output>
26 5b80f544c67f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 52e1975ca4a6895fc2edb0dfde43fe24314bfe51 iuc parents: 20 diff changeset	382 </test>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	383 </tests>
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	384 <help><![CDATA[
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	385 What it does
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	386
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	387 SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	388
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	389 A typical SnpEff use case would be:
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	390
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	391 - Input: The inputs are predicted variants (SNPs, insertions, deletions and MNPs). The input file is usually obtained as a result of a sequencing experiment, and it is usually in variant call format (VCF).
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	392 - Output: SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes). A list of effects and annotations that SnpEff can calculate can be found here.
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	393
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	394 By genetic variant we mean difference between a genome and a "reference" genome. As an example, imagine we are sequencing a "sample". Here "sample" can mean anything that you are interested in studying, from a cell culture, to a mouse or a cancer patient. It is a standard procedure to compare your sample sequences against the corresponding "reference genome". For instance you may compare the cancer patient genome against the "reference genome".
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	395
12 5a29ab10dba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71 iuc parents: 10 diff changeset	396 In a typical sequencing experiment, you will find many places in the genome where your sample differs from the reference genome. These are called "genomic variants" or just "variants".
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	397 Typically, variants are categorized as follows:
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	398
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	399 - SNP (Single-Nucleotide Polymorphism) Reference = 'A', Sample = 'C'
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	400 - Ins (Insertion) Reference = 'A', Sample = 'AGT'
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	401 - Del (Deletion) Reference = 'AC', Sample = 'C'
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	402 - MNP (Multiple-nucleotide polymorphism) Reference = 'ATA', Sample = 'GTC'
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	403 - MIXED (Multiple-nucleotide and an InDel) Reference = 'ATA', Sample = 'GTCAGT'
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	404
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	405 This is not a comprehensive list, it is just to give you an idea.
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	406
12 5a29ab10dba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71 iuc parents: 10 diff changeset	407 Suppose you have a huge file describing all the differences between your sample and the reference genome. But you want to know more about these variants than just their genetic coordinates. E.g.: Are they in a gene? In an exon? Do they change protein coding? Do they cause premature stop codons? SnpEff can help you answer all these questions. The process of adding this information about the variants is called "Annotation".
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	408 SnpEff provides several degrees of annotations, from simple (e.g. which gene is each variant affecting) to extremely complex annotations (e.g. will this non-coding variant affect the expression of a gene?). It should be noted that the more complex the annotations, the more it relies in computational predictions. Such computational predictions can be incorrect, so results from SnpEff (or any prediction algorithm) cannot be trusted blindly, they must be analyzed and independently validated by corresponding wet-lab experiments.
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	409
17 65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 14 diff changeset	410 @SNPEFF_IN_GALAXY_INFO@
65ae79bddc69 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 14 diff changeset	411 @EXTERNAL_DOCUMENTATION@
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	412 ]]>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	413 </help>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	414 <expand macro="citations" />
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	415 </tool>

Mercurial > repos > iuc > snpeff

annotate snpEff.xml @ 29:ca2b512e8d7c draft default tip