snpeff: snpEff.xml annotate

annotate snpEff.xml @ 13:f0ee2b470481 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 0310c734a944901fffb975937b20f55bfc1d9f46

author	iuc
date	Sat, 07 Apr 2018 15:46:09 -0400
parents	5a29ab10dba6
children	85ca751407c3

rev	line source
12 5a29ab10dba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71 iuc parents: 10 diff changeset	1 <tool id="snpEff" name="SnpEff eff:" version="@wrapper_version@.galaxy1">
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[
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	12 snpEff @java_options@ eff
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	13 -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	14 #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	15 -spliceSiteSize "$spliceSiteSize"
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	16 #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	17 #if $spliceRegion.setSpliceRegions == 'yes':
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	18 #if str($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	19 -spliceRegionExonSize $spliceRegion.spliceRegionExonSize
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	20 #end if
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	21 #if str($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	22 -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	23 #end if
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	24 #if str($spliceRegion.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	25 -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	26 #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	27 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	28 #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	29 #echo " "
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	30 #echo ' '.join(str($annotations).split(','))
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	31 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	32 #if $filterOut and str($filterOut) != '':
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	33 #echo " "
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	34 #echo ' '.join(str($filterOut).split(','))
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	35 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	36 #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	37 #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	38 -no $eff
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	39 #end for
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	40 #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	41 #if $transcripts
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	42 -onlyTr '$transcripts'
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 $intervals ### fix this for multiple dataset input
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	45 -interval '$intervals'
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	46 #end if
e8adfc4c0a6b Uploaded iuc parents: diff changeset	47 #if $statsFile:
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	48 -stats '$statsFile'
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	49 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	50 #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	51 ${offset}
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	52 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	53 #if str($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	54 -chr '$chr'
0 e8adfc4c0a6b Uploaded iuc parents: 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 $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	57 ## 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	58 ## 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	59 #if $snpDb.genomeSrc == 'cached':
e8adfc4c0a6b Uploaded iuc parents: diff changeset	60 -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	61 #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	62 #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	63 #for reg in $regs:
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	64 -reg '"${reg}"'
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	65 #end for
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	66 #end if
e8adfc4c0a6b Uploaded iuc parents: diff changeset	67 $snpDb.genomeVersion
e8adfc4c0a6b Uploaded iuc parents: diff changeset	68 #elif $snpDb.genomeSrc == 'history':
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	69 -dataDir '${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	70 #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	71 #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	72 #for reg in $regs:
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	73 -reg '"${reg}"'
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	74 #end for
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	75 #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	76 '${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	77 #elif $snpDb.genomeSrc == 'custom':
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	78 -dataDir '${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	79 -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	80 -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	81 '${snpDb.snpeff_db.metadata.genome_version}'
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	82 #else
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	83 -download
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	84 '$snpDb.genome_version'
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	85 #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	86 '$input' > '$snpeff_output'
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	87 #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	88 &&
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	89 #import os
500832f27cbc Uploaded iuc parents: 0 diff changeset	90 #set $genes_file = str($statsFile) + '.genes.txt'
500832f27cbc Uploaded iuc parents: 0 diff changeset	91 #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	92 mkdir '$statsFile.files_path' &&
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	93 mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#'
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	94 #end if
500832f27cbc Uploaded iuc parents: 0 diff changeset	95 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	96 &&
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	97 ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]"
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	98 sed -i.bak -e 's/^\#\#SnpEffVersion="$\S*\s$/\#\#SnpEffVersion="2.0.5 - real is \1/' '$snpeff_output'
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	99 #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	100 ]]></command>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	101 <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	102 <param name="input" type="data" format="vcf,bed" label="Sequence changes (SNPs, MNPs, InDels)"/>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	103
e8adfc4c0a6b Uploaded iuc parents: diff changeset	104 <param name="inputFormat" type="select" label="Input format">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	105 <option value="vcf" selected="true">VCF</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	106 <option value="bed">BED (Deprecated)</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	107 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	108
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	109 <conditional name="outputConditional">
500832f27cbc Uploaded iuc parents: 0 diff changeset	110 <param name="outputFormat" type="select" label="Output format">
500832f27cbc Uploaded iuc parents: 0 diff changeset	111 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
500832f27cbc Uploaded iuc parents: 0 diff changeset	112 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
500832f27cbc Uploaded iuc parents: 0 diff changeset	113 <option value="bed">BED</option>
500832f27cbc Uploaded iuc parents: 0 diff changeset	114 <option value="bedAnn">BED annotations</option>
500832f27cbc Uploaded iuc parents: 0 diff changeset	115 </param>
500832f27cbc Uploaded iuc parents: 0 diff changeset	116 <when value="vcf" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	117 <when value="gatk">
500832f27cbc Uploaded iuc parents: 0 diff changeset	118 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	119 </when>
500832f27cbc Uploaded iuc parents: 0 diff changeset	120 <when value="bed" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	121 <when value="bedAnn" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	122 </conditional>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	123
e8adfc4c0a6b Uploaded iuc parents: diff changeset	124 <conditional name="snpDb">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	125 <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	126 <!-- 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	127 <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	128 <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	129 <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	130 <option value="custom">Custom snpEff database in your history</option>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	131 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	132 <when value="cached">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	133 <param name="genomeVersion" type="select" label="Genome">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	134 <!--GENOME DESCRIPTION-->
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	135 <options from_data_table="snpeffv_genomedb">
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	136 <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	137 <filter type="unique_value" column="2" />
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	138 </options>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	139 </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	140 <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	141 <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	142 <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	143 <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	144 <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	145 </options>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	146 </param>
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>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	148 </when>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	149 <when value="history">
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	150 <param name="snpeff_db" type="data" format="snpeffdb" label="@snpeff_version@ Genome Data">
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	151 <options options_filter_attribute="metadata.snpeff_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	152 <filter type="add_value" value="@snpeff_version@" />
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	153 </options>
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	154 <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	155 </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	156 <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	157 <!-- 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	158 <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	159 <options>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	160 <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	161 </options>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	162 </param>
7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	163 </section>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	164 </when>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	165 <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	166 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	167 <help>@snpeff_database_url@</help>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	168 <validator type="regex" message="A genome version name is required">\S+</validator>
500832f27cbc Uploaded iuc parents: 0 diff changeset	169 </param>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	170 </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	171 <when value="custom">
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	172 <param name="snpeff_db" type="data" format="snpeffdb" label="@snpeff_version@ Genome Data">
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	173 <options options_filter_attribute="metadata.snpeff_version" >
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	174 <filter type="add_value" value="@snpeff_version@" />
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	175 </options>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	176 <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>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	177 </param>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	178 <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	179 <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	180 <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	181 <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	182 <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	183 <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	184 <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	185 <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	186 <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	187 <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	188 <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	189 <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	190 <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	191 <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	192 <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	193 <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	194 <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	195 <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	196 <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	197 <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	198 <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	199 <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	200 <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	201 <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	202 <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	203 <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	204 </param>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	205 </when>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	206 </conditional>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	207
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	208 <param name="udLength" type="select" label="Upstream / Downstream length" argument="-ud" >
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	209 <option value="0">No upstream / downstream intervals (0 bases)</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	210 <option value="200">200 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	211 <option value="500">500 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	212 <option value="1000">1000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	213 <option value="2000">2000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	214 <option value="5000" selected="true">5000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	215 <option value="10000">10000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	216 <option value="20000">20000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	217 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	218
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	219 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases" argument="-ss">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	220 <option value="1">1 base</option>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	221 <option value="2" selected="true">2 bases</option>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	222 <option value="3">3 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	223 <option value="4">4 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	224 <option value="5">5 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	225 <option value="6">6 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	226 <option value="7">7 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	227 <option value="8">8 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	228 <option value="9">9 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	229 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	230
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	231 <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	232 <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	233 <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	234 <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	235 </param>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	236 <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	237 <when value="yes">
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	238 <param name="spliceRegionExonSize" type="integer" value="" min="1" max="10" optional="true" label="Set size for splice site region within exons. Default: 3 bases" argument="-spliceRegionExonSize"/>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	239 <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" argument="-spliceRegionIntronMin"/>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	240 <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" argument="-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	241 </when>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	242 </conditional>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	243
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	244 <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	245 <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN')</option>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	246 <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	247 <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	248 <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	249 <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	250 <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	251 <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	252 <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	253 <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	254 <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	255 <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	256 <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	257 <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	258 <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	259 <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	260 <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	261 <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	262 <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	263 <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	264 <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	265 <!-- 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	266 <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	267 -->
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	268 </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	269 <!-- -cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples. -->
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	270 <param name="intervals" type="data" format="bed" optional="true" label="Use custom interval file for annotation" argument="-interval"/>
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	271 <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	272 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	273 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	274 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	275 <option value="-no-intron">Do not show INTRON changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	276 <option value="-no-upstream">Do not show UPSTREAM changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	277 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	278 </param>
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	279 <conditional name="filter">
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	280 <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	281 <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	282 <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	283 </param>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	284 <when value="no"/>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	285 <when value="yes">
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	286 <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	287 <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	288 <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	289 <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	290 <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	291 <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	292 <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	293 <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	294 <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	295 <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	296 <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	297 <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	298 <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	299 <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	300 <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	301 <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	302 <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	303 <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	304 <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	305 <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	306 <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	307 <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	308 <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	309 <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	310 <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	311 <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	312 <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	313 <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	314 <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	315 <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	316 <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	317 <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	318 <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	319 <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	320 <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	321 <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	322 <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	323 <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	324 <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	325 <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	326 <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	327 <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	328 <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	329 </param>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	330 </when>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	331 </conditional>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	332
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	333 <param name="offset" type="select" display="radio" label="Chromosomal position" argument="-0 and -1">
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	334 <option value="default" selected="true">Use default (based on input type)</option>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	335 <option value="-0">Force zero-based positions (both input and output)</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	336 <option value="-1">Force one-based positions (both input and output)</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	337 </param>
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	338 <param name="chr" type="text" label="Text to prepend to chromosome name" argument="-chr">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	339 <help>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	340 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	341 You can prepend any string you want to the chromosome name
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	342 </help>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	343 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	344 </param>
10 5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	345 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats" argument="-noStats"/>
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	346 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server" argument="-noLog"/>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	347 </inputs>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	348 <outputs>
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	349 <data name="snpeff_output" format="vcf">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	350 <change_format>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	351 <when input="outputConditional.outputFormat" value="bed" format="bed" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	352 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	353 </change_format>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	354 </data>
7 7adfd0589f49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 5 diff changeset	355 <data name="statsFile" format="html" label="${tool.name} on ${on_string} - stats">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	356 <filter>generate_stats == True</filter>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	357 </data>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	358 </outputs>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	359 <tests>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	360 <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	361 <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	362 <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	363 <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	364 <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	365 <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	366 <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	367 <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	368 <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	369 <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	370 <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	371 <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	372 </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	373 </output>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	374 </test>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	375 </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	376 <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	377
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	378 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	379
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	380 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	381
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	382 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	383
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	384 - 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	385 - 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	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 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	388
12 5a29ab10dba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71 iuc parents: 10 diff changeset	389 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	390 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	391
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	392 - 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	393 - 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	394 - 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	395 - 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	396 - 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	397
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	398 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	399
12 5a29ab10dba6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71 iuc parents: 10 diff changeset	400 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	401 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	402
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	403 @snpeff_in_galaxy_info@
5b4ac70948d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 9 diff changeset	404 @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	405 ]]>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	406 </help>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	407 <expand macro="citations" />
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	408 </tool>

Mercurial > repos > iuc > snpeff

annotate snpEff.xml @ 13:f0ee2b470481 draft