snpeff: snpEff.xml annotate

annotate snpEff.xml @ 3:b24873564cf6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31

author	iuc
date	Tue, 07 Jun 2016 10:03:17 -0400
parents	e09ce114d240
children	698ef30638a8

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" />
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	9 <command>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	10 <![CDATA[
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	11 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/snpEff.jar" eff
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	12 -c "\$SNPEFF_JAR_PATH/snpEff.config"
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':
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	18 #if $spliceRegion.spliceRegionExonSize and str($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	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
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	21 #if $spliceRegion.spliceRegionIntronMin and str($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	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
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	24 #if $spliceRegion.spliceRegionIntronMax and str($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	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
e8adfc4c0a6b Uploaded iuc parents: diff changeset	41 #if str( $transcripts ) != 'None':
e8adfc4c0a6b Uploaded iuc parents: diff changeset	42 -onlyTr $transcripts
e8adfc4c0a6b Uploaded iuc parents: diff changeset	43 #end if
e8adfc4c0a6b Uploaded iuc parents: diff changeset	44 #if str( $intervals ) != 'None': ### fix this for multiple dataset input
e8adfc4c0a6b Uploaded iuc parents: diff changeset	45 -interval $intervals
e8adfc4c0a6b Uploaded iuc parents: diff changeset	46 #end if
e8adfc4c0a6b Uploaded iuc parents: diff changeset	47 #if $statsFile:
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 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() != '':
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 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
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	57 #if $snpDb.genomeSrc == 'cached':
e8adfc4c0a6b Uploaded iuc parents: diff changeset	58 -dataDir ${snpDb.genomeVersion.fields.path}
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	59 #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '':
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	60 #echo " "
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	61 #echo ' '.join(str($snpDb.extra_annotations).split(','))
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	62 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	63 #if $snpDb.regulation and str($snpDb.regulation) != '':
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	64 -reg #echo ' -reg '.join(str($snpDb.regulation).split(','))#
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	65 #end if
e8adfc4c0a6b Uploaded iuc parents: diff changeset	66 $snpDb.genomeVersion
e8adfc4c0a6b Uploaded iuc parents: diff changeset	67 #elif $snpDb.genomeSrc == 'history':
e8adfc4c0a6b Uploaded iuc parents: diff changeset	68 -dataDir ${snpDb.snpeff_db.extra_files_path}
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	69 #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '':
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	70 #set xannotations = [' '] + str($snpDb.extra_annotations).split(',')
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	71 #echo " "
e8adfc4c0a6b Uploaded iuc parents: diff changeset	72 #echo ' -'.join($xannotations)
e8adfc4c0a6b Uploaded iuc parents: diff changeset	73 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	74 #if $snpDb.regulation and str($snpDb.regulation) != '':
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	75 -reg #echo ' -reg '.join(str($snpDb.regulation).split(','))#
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	76 #end if
e8adfc4c0a6b Uploaded iuc parents: diff changeset	77 ${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	78 #else
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	79 -download
e8adfc4c0a6b Uploaded iuc parents: diff changeset	80 $snpDb.genome_version
e8adfc4c0a6b Uploaded iuc parents: diff changeset	81 #end if
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	82 "$input" > "$snpeff_output";
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	83 #if $statsFile:
500832f27cbc Uploaded iuc parents: 0 diff changeset	84 #import os
500832f27cbc Uploaded iuc parents: 0 diff changeset	85 #set $genes_file = str($statsFile) + '.genes.txt'
500832f27cbc Uploaded iuc parents: 0 diff changeset	86 #set $genes_file_name = os.path.split($genes_file)[-1]
500832f27cbc Uploaded iuc parents: 0 diff changeset	87 mkdir $statsFile.files_path;
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	88 mv "$genes_file" #echo os.path.join($statsFile.files_path, $genes_file_name)#;
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	89 #end if
500832f27cbc Uploaded iuc parents: 0 diff changeset	90 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
500832f27cbc Uploaded iuc parents: 0 diff changeset	91 ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]"
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	92 sed -i -e 's/^\#\#SnpEffVersion="$\S*\s$/\#\#SnpEffVersion="2.0.5 - real is \1/' "$snpeff_output"
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	93 #end if
500832f27cbc Uploaded iuc parents: 0 diff changeset	94 ]]>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	95 </command>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	96 <inputs>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	97 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	98
e8adfc4c0a6b Uploaded iuc parents: diff changeset	99 <param name="inputFormat" type="select" label="Input format">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	100 <option value="vcf" selected="true">VCF</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	101 <option value="bed">BED (Deprecated)</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	102 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	103
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	104 <conditional name="outputConditional">
500832f27cbc Uploaded iuc parents: 0 diff changeset	105 <param name="outputFormat" type="select" label="Output format">
500832f27cbc Uploaded iuc parents: 0 diff changeset	106 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
500832f27cbc Uploaded iuc parents: 0 diff changeset	107 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
500832f27cbc Uploaded iuc parents: 0 diff changeset	108 <option value="bed">BED</option>
500832f27cbc Uploaded iuc parents: 0 diff changeset	109 <option value="bedAnn">BED annotations</option>
500832f27cbc Uploaded iuc parents: 0 diff changeset	110 </param>
500832f27cbc Uploaded iuc parents: 0 diff changeset	111 <when value="vcf" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	112 <when value="gatk">
500832f27cbc Uploaded iuc parents: 0 diff changeset	113 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	114 </when>
500832f27cbc Uploaded iuc parents: 0 diff changeset	115 <when value="bed" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	116 <when value="bedAnn" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	117 </conditional>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	118
e8adfc4c0a6b Uploaded iuc parents: diff changeset	119 <conditional name="snpDb">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	120 <param name="genomeSrc" type="select" label="Genome source">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	121 <option value="cached">Locally installed reference genome</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	122 <option value="history">Reference genome from your history</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	123 <option value="named">Named on demand</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	124 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	125 <when value="cached">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	126 <param name="genomeVersion" type="select" label="Genome">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	127 <!--GENOME DESCRIPTION-->
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	128 <options from_data_table="snpeffv_genomedb">
500832f27cbc Uploaded iuc parents: 0 diff changeset	129 <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/>
500832f27cbc Uploaded iuc parents: 0 diff changeset	130 <filter type="unique_value" column="2" />
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	131 </options>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	132 </param>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	133 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	134 <help>These are available for only a few genomes</help>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	135 <options from_data_table="snpeffv_annotations">
500832f27cbc Uploaded iuc parents: 0 diff changeset	136 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	137 <filter type="unique_value" column="3" />
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	138 </options>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	139 </param>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	140 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	141 <help>These are available for only a few genomes</help>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	142 <options from_data_table="snpeffv_regulationdb">
500832f27cbc Uploaded iuc parents: 0 diff changeset	143 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	144 <filter type="unique_value" column="3" />
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	145 </options>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	146 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	147 </when>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	148 <when value="history">
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	149 <param format="snpeffdb" name="snpeff_db" type="data" label="@SNPEFF_VERSION@ Genome Data">
500832f27cbc Uploaded iuc parents: 0 diff changeset	150 <options options_filter_attribute="metadata.snpeff_version" >
500832f27cbc Uploaded iuc parents: 0 diff changeset	151 <filter type="add_value" value="@SNPEFF_VERSION@" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	152 </options>
500832f27cbc Uploaded iuc parents: 0 diff changeset	153 <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>
500832f27cbc Uploaded iuc parents: 0 diff changeset	154 </param>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	155 <!-- From metadata -->
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	156 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	157 <help>These are available for only a few genomes</help>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	158 <options>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	159 <filter type="data_meta" ref="snpeff_db" key="annotation" />
e8adfc4c0a6b Uploaded iuc parents: diff changeset	160 </options>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	161 </param>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	162 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	163 <help>These are available for only a few genomes</help>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	164 <options>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	165 <filter type="data_meta" ref="snpeff_db" key="regulation" />
e8adfc4c0a6b Uploaded iuc parents: diff changeset	166 </options>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	167 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	168 </when>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	169 <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	170 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	171 <help>@SNPEFF_DATABASE_URL@</help>
500832f27cbc Uploaded iuc parents: 0 diff changeset	172 <validator type="regex" message="A genome version name is required">\S+</validator>
500832f27cbc Uploaded iuc parents: 0 diff changeset	173 </param>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	174 </when>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	175 </conditional>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	176
e8adfc4c0a6b Uploaded iuc parents: diff changeset	177 <param name="udLength" type="select" label="Upstream / Downstream length">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	178 <option value="0">No upstream / downstream intervals (0 bases)</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	179 <option value="200">200 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	180 <option value="500">500 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	181 <option value="1000">1000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	182 <option value="2000">2000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	183 <option value="5000" selected="true">5000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	184 <option value="10000">10000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	185 <option value="20000">20000 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	186 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	187
e8adfc4c0a6b Uploaded iuc parents: diff changeset	188 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases" help="Default: 2">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	189 <option value="1">1 base</option>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	190 <option value="2" selected="true">2 bases</option>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	191 <option value="3">3 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	192 <option value="4">4 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	193 <option value="5">5 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	194 <option value="6">6 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	195 <option value="7">7 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	196 <option value="8">8 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	197 <option value="9">9 bases</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	198 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	199
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	200 <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	201 <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	202 <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	203 <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	204 </param>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	205 <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	206 <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	207 <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	208 <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	209 <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	210 </when>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	211 </conditional>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	212
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	213 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	214 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	215 <option value="-canon">Only use canonical transcripts</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	216 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	217 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	218 <option value="-oicr">Add OICR tag in VCF file</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	219 <option value="-onlyReg">Only use regulation tracks</option>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	220 <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>
500832f27cbc Uploaded iuc parents: 0 diff changeset	221 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option>
500832f27cbc Uploaded iuc parents: 0 diff changeset	222 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option>
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	223 <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN').</option>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	224 <option value="-noHgvs">Do not add HGVS annotations.</option>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	225 <option value="-noLof">Do not add LOF and NMD annotations.</option>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	226 <option value="-noShiftHgvs">Do not shift variants according to HGVS notation (most 3prime end).</option>
b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	227 <option value="-oicr">Add OICR tag in VCF file. Default: false</option>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	228 </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	229 <!-- -cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples. -->
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	230 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	231 <param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file." help="Format is one transcript ID per line."/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	232 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	233 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	234 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	235 <option value="-no-intron">Do not show INTRON changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	236 <option value="-no-upstream">Do not show UPSTREAM changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	237 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	238 </param>
2 e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	239 <conditional name="filter">
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	240 <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	241 <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	242 <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	243 </param>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	244 <when value="no"/>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	245 <when value="yes">
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	246 <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	247 <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	248 <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	249 <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	250 <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	251 <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	252 <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	253 <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	254 <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	255 <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	256 <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	257 <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	258 <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	259 <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	260 <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	261 <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	262 <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	263 <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	264 <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	265 <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	266 <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	267 <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	268 <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	269 <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	270 <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	271 <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	272 <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	273 <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	274 <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	275 <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	276 <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	277 <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	278 <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	279 <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	280 <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	281 <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	282 <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	283 <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	284 <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	285 <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	286 <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	287 <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	288 <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	289
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	290 </param>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	291 </when>
e09ce114d240 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff iuc parents: 1 diff changeset	292 </conditional>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	293
e8adfc4c0a6b Uploaded iuc parents: diff changeset	294 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	295 <option value="default" selected="true">Use default (based on input type)</option>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	296 <option value="-0">Force zero-based positions (both input and output)</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	297 <option value="-1">Force one-based positions (both input and output)</option>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	298 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	299 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	300 <help>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	301 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
e8adfc4c0a6b Uploaded iuc parents: diff changeset	302 You can prepend any string you want to the chromosome name.
e8adfc4c0a6b Uploaded iuc parents: diff changeset	303 </help>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	304 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	305 </param>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	306 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	307 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server"/>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	308 </inputs>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	309 <outputs>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	310 <data format="vcf" name="snpeff_output" >
e8adfc4c0a6b Uploaded iuc parents: diff changeset	311 <change_format>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	312 <when input="outputConditional.outputFormat" value="bed" format="bed" />
500832f27cbc Uploaded iuc parents: 0 diff changeset	313 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	314 </change_format>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	315 </data>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	316 <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats">
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	317 <filter>generate_stats == True</filter>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	318 </data>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	319 </outputs>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	320 <tests>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	321 <!-- Check that an effect was added in out VCF -->
e8adfc4c0a6b Uploaded iuc parents: diff changeset	322 <!-- Check for a HTML header indicating that this was successful -->
e8adfc4c0a6b Uploaded iuc parents: diff changeset	323 <!--
e8adfc4c0a6b Uploaded iuc parents: diff changeset	324 <output name="statsFile">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	325 <assert_contents>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	326 <has_text text="SnpEff: Variant analysis" />
e8adfc4c0a6b Uploaded iuc parents: diff changeset	327 </assert_contents>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	328 </output>
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	329 -->
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	330 <!-- Setting filterOut throws exception in twilltestcase.py
e8adfc4c0a6b Uploaded iuc parents: diff changeset	331 <test>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	332 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	333 <param name="inputFormat" value="vcf"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	334 <param name="outputFormat" value="vcf"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	335 <param name="genomeSrc" value="named"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	336 <param name="genome_version" value="testCase"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	337 <param name="udLength" value="0"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	338 <param name="generate_stats" value="False"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	339 <param name="filterOut" value="+-no-upstream"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	340 <output name="snpeff_output">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	341 <assert_contents>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	342 <has_text text="EFF=" />
e8adfc4c0a6b Uploaded iuc parents: diff changeset	343 </assert_contents>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	344 </output>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	345 </test>
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	346 -->
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	347
e8adfc4c0a6b Uploaded iuc parents: diff changeset	348 <test>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	349 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	350 <param name="inputFormat" value="vcf"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	351 <param name="outputFormat" value="vcf"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	352 <param name="genomeSrc" value="named"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	353 <param name="genome_version" value="testCase"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	354 <param name="udLength" value="0"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	355 <!--
e8adfc4c0a6b Uploaded iuc parents: diff changeset	356 <param name="filterOut" value=""/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	357 -->
e8adfc4c0a6b Uploaded iuc parents: diff changeset	358 <param name="generate_stats" value="False"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	359 <output name="snpeff_output">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	360 <assert_contents>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	361 <!-- Check that deleletions were evaluated -->
e8adfc4c0a6b Uploaded iuc parents: diff changeset	362 <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" />
e8adfc4c0a6b Uploaded iuc parents: diff changeset	363 <!-- Check that insertion on last line was NOT evaluated -->
e8adfc4c0a6b Uploaded iuc parents: diff changeset	364 <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" />
e8adfc4c0a6b Uploaded iuc parents: diff changeset	365 </assert_contents>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	366 </output>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	367 </test>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	368
e8adfc4c0a6b Uploaded iuc parents: diff changeset	369 <!-- Check that NO UPSTREAM effect was added -->
e8adfc4c0a6b Uploaded iuc parents: diff changeset	370 <!-- Setting filterOut throws exception in twilltestcase.py
e8adfc4c0a6b Uploaded iuc parents: diff changeset	371 <test>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	372 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	373 <param name="inputFormat" value="vcf"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	374 <param name="outputFormat" value="vcf"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	375 <param name="genomeSrc" value="named"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	376 <param name="genome_version" value="testCase"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	377 <param name="udLength" value="0"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	378 <param name="filterOut" value="+-no-upstream"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	379 <param name="generate_stats" value="False"/>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	380 <output name="snpeff_output">
e8adfc4c0a6b Uploaded iuc parents: diff changeset	381 <assert_contents>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	382 <not_has_text text="UPSTREAM" />
e8adfc4c0a6b Uploaded iuc parents: diff changeset	383 </assert_contents>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	384 </output>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	385 </test>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	386 -->
e8adfc4c0a6b Uploaded iuc parents: diff changeset	387
e8adfc4c0a6b Uploaded iuc parents: diff changeset	388 </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	389 <help><![CDATA[
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	390
e8adfc4c0a6b Uploaded iuc parents: diff changeset	391 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
e8adfc4c0a6b Uploaded iuc parents: diff changeset	392
e8adfc4c0a6b Uploaded iuc parents: diff changeset	393 @EXTERNAL_DOCUMENTATION@
e8adfc4c0a6b Uploaded iuc parents: diff changeset	394
3 b24873564cf6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 2 diff changeset	395 ]]>
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	396 </help>
1 500832f27cbc Uploaded iuc parents: 0 diff changeset	397 <expand macro="citations" />
0 e8adfc4c0a6b Uploaded iuc parents: diff changeset	398 </tool>
e8adfc4c0a6b Uploaded iuc parents: diff changeset	399

Mercurial > repos > iuc > snpeff

annotate snpEff.xml @ 3:b24873564cf6 draft