snpeff: snpEff.xml annotate

annotate snpEff.xml @ 7:7adfd0589f49 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1

author	iuc
date	Tue, 18 Apr 2017 09:33:56 -0400
parents	2950d5afa3fe
children	ce135864629c

rev	line source
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.0">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	2 <description>Variant effect and annotation</description>
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>
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	6 <expand macro="requirements" />
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	7 <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	8 <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	9 <command><![CDATA[
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	10 snpEff -Xmx8g eff
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	11 -i $inputFormat -o ${outputConditional.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	12 #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	13 -spliceSiteSize "$spliceSiteSize"
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	14 #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	15 #if $spliceRegion.setSpliceRegions == 'yes':
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	16 #if str($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	17 -spliceRegionExonSize $spliceRegion.spliceRegionExonSize
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	18 #end if
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	19 #if str($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	20 -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	21 #end if
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	22 #if str($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	23 -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	24 #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	25 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	26 #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	27 #echo " "
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	28 #echo ' '.join(str($annotations).split(','))
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	29 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	30 #if $filterOut and str($filterOut) != '':
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	31 #echo " "
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	32 #echo ' '.join(str($filterOut).split(','))
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	33 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	34 #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	35 #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	36 -no $eff
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	37 #end for
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	38 #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	39 #if $transcripts
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	40 -onlyTr '$transcripts'
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	41 #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	42 #if $intervals ### fix this for multiple dataset input
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	43 -interval '$intervals'
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	44 #end if
e8adfc4c0a6b Uploaded iuc parents: diff changeset	45 #if $statsFile:
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	46 -stats '$statsFile'
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	47 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	48 #if str($offset) != 'default':
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	49 ${offset}
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	50 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	51 #if str($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	52 -chr '$chr'
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	53 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	54 $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	55 ## 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	56 ## 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	57 #if $snpDb.genomeSrc == 'cached':
e8adfc4c0a6b Uploaded iuc parents: diff changeset	58 -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	59 #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	60 #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	61 #for reg in $regs:
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	62 -reg '"${reg}"'
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	63 #end for
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	64 #end if
e8adfc4c0a6b Uploaded iuc parents: diff changeset	65 $snpDb.genomeVersion
e8adfc4c0a6b Uploaded iuc parents: diff changeset	66 #elif $snpDb.genomeSrc == 'history':
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	67 -dataDir '${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	68 #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	69 #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	70 #for reg in $regs:
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	71 -reg '"${reg}"'
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	72 #end for
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	73 #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	74 '${snpDb.snpeff_db.metadata.genome_version}'
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	75 #else
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	76 -download
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	77 '$snpDb.genome_version'
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 '$input' > '$snpeff_output'
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	80 #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	81 &&
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	82 #import os
500832f27cbc Uploaded iuc parents: 0 diff changeset	83 #set $genes_file = str($statsFile) + '.genes.txt'
500832f27cbc Uploaded iuc parents: 0 diff changeset	84 #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	85 mkdir '$statsFile.files_path' &&
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	86 mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#'
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	87 #end if
500832f27cbc Uploaded iuc parents: 0 diff changeset	88 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	89 &&
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	90 ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]"
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	91 sed -i.bak -e 's/^\#\#SnpEffVersion="$\S*\s$/\#\#SnpEffVersion="2.0.5 - real is \1/' '$snpeff_output'
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	92 #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	93 ]]></command>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	94 <inputs>
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	95 <param name="input" type="data" format="vcf,tabular,pileup,bed" label="Sequence changes (SNPs, MNPs, InDels)"/>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	96
e8adfc4c0a6b Uploaded iuc parents: diff changeset	97 <param name="inputFormat" type="select" label="Input format">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	98 <option value="vcf" selected="true">VCF</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	99 <option value="bed">BED (Deprecated)</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	100 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	101
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	102 <conditional name="outputConditional">
500832f27cbc Uploaded iuc parents: 0 diff changeset	103 <param name="outputFormat" type="select" label="Output format">
500832f27cbc Uploaded iuc parents: 0 diff changeset	104 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
500832f27cbc Uploaded iuc parents: 0 diff changeset	105 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
500832f27cbc Uploaded iuc parents: 0 diff changeset	106 <option value="bed">BED</option>
500832f27cbc Uploaded iuc parents: 0 diff changeset	107 <option value="bedAnn">BED annotations</option>
500832f27cbc Uploaded iuc parents: 0 diff changeset	108 </param>
500832f27cbc Uploaded iuc parents: 0 diff changeset	109 <when value="vcf" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	110 <when value="gatk">
500832f27cbc Uploaded iuc parents: 0 diff changeset	111 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	112 </when>
500832f27cbc Uploaded iuc parents: 0 diff changeset	113 <when value="bed" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	114 <when value="bedAnn" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	115 </conditional>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	116
e8adfc4c0a6b Uploaded iuc parents: diff changeset	117 <conditional name="snpDb">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	118 <param name="genomeSrc" type="select" label="Genome source">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	119 <option value="cached">Locally installed reference genome</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	120 <option value="history">Reference genome from your history</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	121 <option value="named">Named on demand</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	122 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	123 <when value="cached">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	124 <param name="genomeVersion" type="select" label="Genome">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	125 <!--GENOME DESCRIPTION-->
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	126 <options from_data_table="snpeffv_genomedb">
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	127 <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	128 <filter type="unique_value" column="2" />
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	129 </options>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	130 </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	131 <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	132 <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	133 <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	134 <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	135 <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	136 </options>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	137 </param>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	138 </section>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	139 </when>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	140 <when value="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	141 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	142 <options options_filter_attribute="metadata.snpeff_version" >
500832f27cbc Uploaded iuc parents: 0 diff changeset	143 <filter type="add_value" value="@SNPEFF_VERSION@" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	144 </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	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">
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	157 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	158 <help>@SNPEFF_DATABASE_URL@</help>
500832f27cbc Uploaded iuc parents: 0 diff changeset	159 <validator type="regex" message="A genome version name is required">\S+</validator>
500832f27cbc Uploaded iuc parents: 0 diff changeset	160 </param>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	161 </when>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	162 </conditional>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	163
e8adfc4c0a6b Uploaded iuc parents: diff changeset	164 <param name="udLength" type="select" label="Upstream / Downstream length">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	165 <option value="0">No upstream / downstream intervals (0 bases)</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	166 <option value="200">200 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	167 <option value="500">500 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	168 <option value="1000">1000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	169 <option value="2000">2000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	170 <option value="5000" selected="true">5000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	171 <option value="10000">10000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	172 <option value="20000">20000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	173 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	174
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	175 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	176 <option value="1">1 base</option>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	177 <option value="2" selected="true">2 bases</option>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	178 <option value="3">3 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	179 <option value="4">4 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	180 <option value="5">5 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	181 <option value="6">6 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	182 <option value="7">7 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	183 <option value="8">8 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	184 <option value="9">9 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	185 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	186
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	187 <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	188 <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	189 <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	190 <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	191 </param>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	192 <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	193 <when value="yes">
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	194 <param name="spliceRegionExonSize" type="integer" value="" min="1" max="10" optional="true" label="Set size for splice site region within exons. Default: 3 bases"/>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	195 <param name="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"/>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	196 <param name="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"/>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	197 </when>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	198 </conditional>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	199
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	200 <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	201 <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN')</option>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	202 <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	203 <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	204 <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	205 <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	206 <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	207 <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	208 <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	209 <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	210 <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	211 <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	212 <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	213 <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	214 <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	215 <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	216 <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	217 <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	218 <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	219 <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	220 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	221 <!-- onlyReg option results in ifrequent exceptions with version 4.3k
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	222 <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	223 -->
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	224 </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	225 <!-- -cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples. -->
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	226 <param name="intervals" type="data" format="bed" optional="true" label="Use custom interval file for annotation"/>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	227 <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	228 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	229 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	230 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	231 <option value="-no-intron">Do not show INTRON changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	232 <option value="-no-upstream">Do not show UPSTREAM changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	233 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	234 </param>
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	235 <conditional name="filter">
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	236 <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	237 <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	238 <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	239 </param>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	240 <when value="no"/>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	241 <when value="yes">
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	242 <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	243 <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	244 <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	245 <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	246 <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	247 <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	248 <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	249 <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	250 <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	251 <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	252 <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	253 <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	254 <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	255 <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	256 <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	257 <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	258 <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	259 <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	260 <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	261 <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	262 <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	263 <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	264 <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	265 <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	266 <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	267 <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	268 <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	269 <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	270 <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	271 <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	272 <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	273 <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	274 <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	275 <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	276 <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	277 <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	278 <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	279 <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	280 <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	281 <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	282 <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	283 <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	284 <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	285 </param>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	286 </when>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	287 </conditional>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	288
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	289 <param name="offset" type="select" display="radio" label="Chromosomal position">
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	290 <option value="default" selected="true">Use default (based on input type)</option>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	291 <option value="-0">Force zero-based positions (both input and output)</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	292 <option value="-1">Force one-based positions (both input and output)</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	293 </param>
5 2950d5afa3fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 4 diff changeset	294 <param name="chr" type="text" label="Text to prepend to chromosome name">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	295 <help>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	296 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	297 You can prepend any string you want to the chromosome name
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	298 </help>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	299 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	300 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	301 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	302 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server"/>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	303 </inputs>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	304 <outputs>
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	305 <data name="snpeff_output" format="vcf">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	306 <change_format>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	307 <when input="outputConditional.outputFormat" value="bed" format="bed" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	308 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	309 </change_format>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	310 </data>
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	311 <data name="statsFile" format="html" label="${tool.name} on ${on_string} - stats">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	312 <filter>generate_stats == True</filter>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	313 </data>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	314 </outputs>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	315 <tests>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	316 <test>
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	317 <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	318 <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	319 <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	320 <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	321 <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	322 <param name="udLength" value="0"/>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	323 <param name="generate_stats" value="False"/>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	324 <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	325 <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	326 <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	327 <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	328 </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	329 </output>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	330 </test>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	331 </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	332 <help><![CDATA[
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	333 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
e8adfc4c0a6b Uploaded iuc parents: diff changeset	334
e8adfc4c0a6b Uploaded iuc parents: diff changeset	335 @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	336 ]]>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	337 </help>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	338 <expand macro="citations" />
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	339 </tool>

Mercurial > repos > iuc > snpeff

annotate snpEff.xml @ 7:7adfd0589f49 draft