snpeff: snpEff.xml annotate

annotate snpEff.xml @ 6:9ec1cb6f760d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e

author	iuc
date	Tue, 13 Oct 2015 17:30:57 -0400
parents	92b80578fa22
children	aaa749ea91a2

rev	line source
6 9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.1">
0 39bac90c773d Uploaded iuc parents: diff changeset	2 <description>Variant effect and annotation</description>
39bac90c773d Uploaded iuc parents: diff changeset	3 <macros>
39bac90c773d Uploaded iuc parents: diff changeset	4 <import>snpEff_macros.xml</import>
39bac90c773d Uploaded iuc parents: diff changeset	5 </macros>
5 92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 2 diff changeset	6 <expand macro="requirements" />
92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 2 diff changeset	7 <expand macro="stdio" />
0 39bac90c773d Uploaded iuc parents: diff changeset	8 <command>
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	9 <![CDATA[
5 92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 2 diff changeset	10 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff
92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 2 diff changeset	11 -c \$SNPEFF_JAR_PATH/snpEff.config
0 39bac90c773d Uploaded iuc parents: diff changeset	12 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
39bac90c773d Uploaded iuc parents: diff changeset	13 #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
39bac90c773d Uploaded iuc parents: diff changeset	14 -spliceSiteSize $spliceSiteSize
39bac90c773d Uploaded iuc parents: diff changeset	15 #end if
39bac90c773d Uploaded iuc parents: diff changeset	16 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
5 92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 2 diff changeset	17 $filterHomHet
0 39bac90c773d Uploaded iuc parents: diff changeset	18 #end if
39bac90c773d Uploaded iuc parents: diff changeset	19 #if $annotations and $annotations.__str__ != '':
39bac90c773d Uploaded iuc parents: diff changeset	20 #echo " "
39bac90c773d Uploaded iuc parents: diff changeset	21 #echo ' '.join($annotations.__str__.split(','))
39bac90c773d Uploaded iuc parents: diff changeset	22 #end if
39bac90c773d Uploaded iuc parents: diff changeset	23 #if $filterOut and $filterOut.__str__ != '':
39bac90c773d Uploaded iuc parents: diff changeset	24 #echo " "
39bac90c773d Uploaded iuc parents: diff changeset	25 #echo ' '.join($filterOut.__str__.split(','))
39bac90c773d Uploaded iuc parents: diff changeset	26 #end if
6 9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	27 #if $filter.specificEffects == 'yes' and $filter.effects:
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	28 #for $eff in str($filter.effects).split(','):
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	29 -no $eff
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	30 #end for
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	31 #end if
0 39bac90c773d Uploaded iuc parents: diff changeset	32 #if str( $transcripts ) != 'None':
39bac90c773d Uploaded iuc parents: diff changeset	33 -onlyTr $transcripts
39bac90c773d Uploaded iuc parents: diff changeset	34 #end if
39bac90c773d Uploaded iuc parents: diff changeset	35 #if str( $intervals ) != 'None': ### fix this for multiple dataset input
39bac90c773d Uploaded iuc parents: diff changeset	36 -interval $intervals
39bac90c773d Uploaded iuc parents: diff changeset	37 #end if
39bac90c773d Uploaded iuc parents: diff changeset	38 #if $statsFile:
5 92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 2 diff changeset	39 -stats $statsFile
0 39bac90c773d Uploaded iuc parents: diff changeset	40 #end if
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	41 #if $offset.__str__ != 'default':
5 92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 2 diff changeset	42 ${offset}
0 39bac90c773d Uploaded iuc parents: diff changeset	43 #end if
39bac90c773d Uploaded iuc parents: diff changeset	44 #if $chr.__str__.strip() != '':
5 92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 2 diff changeset	45 -chr "$chr"
0 39bac90c773d Uploaded iuc parents: diff changeset	46 #end if
5 92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 2 diff changeset	47 $noLog
0 39bac90c773d Uploaded iuc parents: diff changeset	48 #if $snpDb.genomeSrc == 'cached':
39bac90c773d Uploaded iuc parents: diff changeset	49 -dataDir ${snpDb.genomeVersion.fields.path}
39bac90c773d Uploaded iuc parents: diff changeset	50 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
39bac90c773d Uploaded iuc parents: diff changeset	51 #echo " "
39bac90c773d Uploaded iuc parents: diff changeset	52 #echo ' '.join($snpDb.extra_annotations.__str__.split(','))
39bac90c773d Uploaded iuc parents: diff changeset	53 #end if
39bac90c773d Uploaded iuc parents: diff changeset	54 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
39bac90c773d Uploaded iuc parents: diff changeset	55 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
39bac90c773d Uploaded iuc parents: diff changeset	56 #end if
39bac90c773d Uploaded iuc parents: diff changeset	57 $snpDb.genomeVersion
39bac90c773d Uploaded iuc parents: diff changeset	58 #elif $snpDb.genomeSrc == 'history':
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	59 -dataDir ${snpDb.snpeff_db.extra_files_path}
0 39bac90c773d Uploaded iuc parents: diff changeset	60 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
39bac90c773d Uploaded iuc parents: diff changeset	61 #set xannotations = [' '] + $snpDb.extra_annotations.__str__.split(',')
39bac90c773d Uploaded iuc parents: diff changeset	62 #echo " "
39bac90c773d Uploaded iuc parents: diff changeset	63 #echo ' -'.join($xannotations)
39bac90c773d Uploaded iuc parents: diff changeset	64 #end if
39bac90c773d Uploaded iuc parents: diff changeset	65 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
39bac90c773d Uploaded iuc parents: diff changeset	66 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
39bac90c773d Uploaded iuc parents: diff changeset	67 #end if
39bac90c773d Uploaded iuc parents: diff changeset	68 ${snpDb.snpeff_db.metadata.genome_version}
5 92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 2 diff changeset	69 #else
0 39bac90c773d Uploaded iuc parents: diff changeset	70 -download
39bac90c773d Uploaded iuc parents: diff changeset	71 $snpDb.genome_version
39bac90c773d Uploaded iuc parents: diff changeset	72 #end if
39bac90c773d Uploaded iuc parents: diff changeset	73 $input > $snpeff_output ;
39bac90c773d Uploaded iuc parents: diff changeset	74 #if $statsFile:
39bac90c773d Uploaded iuc parents: diff changeset	75 #import os
39bac90c773d Uploaded iuc parents: diff changeset	76 #set $genes_file = str($statsFile) + '.genes.txt'
39bac90c773d Uploaded iuc parents: diff changeset	77 #set $genes_file_name = os.path.split($genes_file)[-1]
39bac90c773d Uploaded iuc parents: diff changeset	78 mkdir $statsFile.files_path;
39bac90c773d Uploaded iuc parents: diff changeset	79 mv $genes_file #echo os.path.join($statsFile.files_path, $genes_file_name)#;
39bac90c773d Uploaded iuc parents: diff changeset	80 #end if
39bac90c773d Uploaded iuc parents: diff changeset	81 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
39bac90c773d Uploaded iuc parents: diff changeset	82 ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]"
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	83 sed -i -e 's/^\#\#SnpEffVersion="$\S*\s$/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output
0 39bac90c773d Uploaded iuc parents: diff changeset	84 #end if
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	85 ]]>
0 39bac90c773d Uploaded iuc parents: diff changeset	86 </command>
39bac90c773d Uploaded iuc parents: diff changeset	87 <inputs>
39bac90c773d Uploaded iuc parents: diff changeset	88 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
39bac90c773d Uploaded iuc parents: diff changeset	89
39bac90c773d Uploaded iuc parents: diff changeset	90 <param name="inputFormat" type="select" label="Input format">
39bac90c773d Uploaded iuc parents: diff changeset	91 <option value="vcf" selected="true">VCF</option>
39bac90c773d Uploaded iuc parents: diff changeset	92 <option value="txt">Tabular (Deprecated)</option>
39bac90c773d Uploaded iuc parents: diff changeset	93 <option value="pileup">Pileup (Deprecated)</option>
39bac90c773d Uploaded iuc parents: diff changeset	94 <option value="bed">BED (Deprecated)</option>
39bac90c773d Uploaded iuc parents: diff changeset	95 </param>
39bac90c773d Uploaded iuc parents: diff changeset	96
39bac90c773d Uploaded iuc parents: diff changeset	97 <conditional name="outputConditional">
39bac90c773d Uploaded iuc parents: diff changeset	98 <param name="outputFormat" type="select" label="Output format">
39bac90c773d Uploaded iuc parents: diff changeset	99 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
39bac90c773d Uploaded iuc parents: diff changeset	100 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
39bac90c773d Uploaded iuc parents: diff changeset	101 <option value="txt">Tabular</option>
39bac90c773d Uploaded iuc parents: diff changeset	102 <option value="bed">BED</option>
39bac90c773d Uploaded iuc parents: diff changeset	103 <option value="bedAnn">BED annotations</option>
39bac90c773d Uploaded iuc parents: diff changeset	104 </param>
39bac90c773d Uploaded iuc parents: diff changeset	105 <when value="vcf" />
39bac90c773d Uploaded iuc parents: diff changeset	106 <when value="gatk">
39bac90c773d Uploaded iuc parents: diff changeset	107 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
39bac90c773d Uploaded iuc parents: diff changeset	108 </when>
39bac90c773d Uploaded iuc parents: diff changeset	109 <when value="txt" />
39bac90c773d Uploaded iuc parents: diff changeset	110 <when value="bed" />
39bac90c773d Uploaded iuc parents: diff changeset	111 <when value="bedAnn" />
39bac90c773d Uploaded iuc parents: diff changeset	112 </conditional>
39bac90c773d Uploaded iuc parents: diff changeset	113
39bac90c773d Uploaded iuc parents: diff changeset	114 <conditional name="snpDb">
39bac90c773d Uploaded iuc parents: diff changeset	115 <param name="genomeSrc" type="select" label="Genome source">
39bac90c773d Uploaded iuc parents: diff changeset	116 <option value="cached">Locally installed reference genome</option>
39bac90c773d Uploaded iuc parents: diff changeset	117 <option value="history">Reference genome from your history</option>
39bac90c773d Uploaded iuc parents: diff changeset	118 <option value="named">Named on demand</option>
39bac90c773d Uploaded iuc parents: diff changeset	119 </param>
39bac90c773d Uploaded iuc parents: diff changeset	120 <when value="cached">
39bac90c773d Uploaded iuc parents: diff changeset	121 <param name="genomeVersion" type="select" label="Genome">
39bac90c773d Uploaded iuc parents: diff changeset	122 <!--GENOME DESCRIPTION-->
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	123 <options from_data_table="snpeffv_genomedb">
114f423f99c0 Uploaded iuc parents: 0 diff changeset	124 <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/>
114f423f99c0 Uploaded iuc parents: 0 diff changeset	125 <filter type="unique_value" column="2" />
0 39bac90c773d Uploaded iuc parents: diff changeset	126 </options>
39bac90c773d Uploaded iuc parents: diff changeset	127 </param>
39bac90c773d Uploaded iuc parents: diff changeset	128 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
39bac90c773d Uploaded iuc parents: diff changeset	129 <help>These are available for only a few genomes</help>
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	130 <options from_data_table="snpeffv_annotations">
114f423f99c0 Uploaded iuc parents: 0 diff changeset	131 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
114f423f99c0 Uploaded iuc parents: 0 diff changeset	132 <filter type="unique_value" column="3" />
0 39bac90c773d Uploaded iuc parents: diff changeset	133 </options>
39bac90c773d Uploaded iuc parents: diff changeset	134 </param>
39bac90c773d Uploaded iuc parents: diff changeset	135 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation">
39bac90c773d Uploaded iuc parents: diff changeset	136 <help>These are available for only a few genomes</help>
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	137 <options from_data_table="snpeffv_regulationdb">
114f423f99c0 Uploaded iuc parents: 0 diff changeset	138 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
114f423f99c0 Uploaded iuc parents: 0 diff changeset	139 <filter type="unique_value" column="3" />
0 39bac90c773d Uploaded iuc parents: diff changeset	140 </options>
39bac90c773d Uploaded iuc parents: diff changeset	141 </param>
39bac90c773d Uploaded iuc parents: diff changeset	142 </when>
39bac90c773d Uploaded iuc parents: diff changeset	143 <when value="history">
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	144 <param format="snpeffdb" name="snpeff_db" type="data" label="@SNPEFF_VERSION@ Genome Data">
114f423f99c0 Uploaded iuc parents: 0 diff changeset	145 <options options_filter_attribute="metadata.snpeff_version" >
114f423f99c0 Uploaded iuc parents: 0 diff changeset	146 <filter type="add_value" value="@SNPEFF_VERSION@" />
114f423f99c0 Uploaded iuc parents: 0 diff changeset	147 </options>
114f423f99c0 Uploaded iuc parents: 0 diff changeset	148 <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>
114f423f99c0 Uploaded iuc parents: 0 diff changeset	149 </param>
0 39bac90c773d Uploaded iuc parents: diff changeset	150 <!-- From metadata -->
39bac90c773d Uploaded iuc parents: diff changeset	151 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
39bac90c773d Uploaded iuc parents: diff changeset	152 <help>These are available for only a few genomes</help>
39bac90c773d Uploaded iuc parents: diff changeset	153 <options>
39bac90c773d Uploaded iuc parents: diff changeset	154 <filter type="data_meta" ref="snpeff_db" key="annotation" />
39bac90c773d Uploaded iuc parents: diff changeset	155 </options>
39bac90c773d Uploaded iuc parents: diff changeset	156 </param>
39bac90c773d Uploaded iuc parents: diff changeset	157 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation">
39bac90c773d Uploaded iuc parents: diff changeset	158 <help>These are available for only a few genomes</help>
39bac90c773d Uploaded iuc parents: diff changeset	159 <options>
39bac90c773d Uploaded iuc parents: diff changeset	160 <filter type="data_meta" ref="snpeff_db" key="regulation" />
39bac90c773d Uploaded iuc parents: diff changeset	161 </options>
39bac90c773d Uploaded iuc parents: diff changeset	162 </param>
39bac90c773d Uploaded iuc parents: diff changeset	163 </when>
39bac90c773d Uploaded iuc parents: diff changeset	164 <when value="named">
6 9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	165 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	166 <help>@SNPEFF_DATABASE_URL@</help>
114f423f99c0 Uploaded iuc parents: 0 diff changeset	167 <validator type="regex" message="A genome version name is required">\S+</validator>
114f423f99c0 Uploaded iuc parents: 0 diff changeset	168 </param>
0 39bac90c773d Uploaded iuc parents: diff changeset	169 </when>
39bac90c773d Uploaded iuc parents: diff changeset	170 </conditional>
39bac90c773d Uploaded iuc parents: diff changeset	171
39bac90c773d Uploaded iuc parents: diff changeset	172 <param name="udLength" type="select" label="Upstream / Downstream length">
39bac90c773d Uploaded iuc parents: diff changeset	173 <option value="0">No upstream / downstream intervals (0 bases)</option>
39bac90c773d Uploaded iuc parents: diff changeset	174 <option value="200">200 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	175 <option value="500">500 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	176 <option value="1000">1000 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	177 <option value="2000">2000 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	178 <option value="5000" selected="true">5000 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	179 <option value="10000">10000 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	180 <option value="20000">20000 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	181 </param>
39bac90c773d Uploaded iuc parents: diff changeset	182
39bac90c773d Uploaded iuc parents: diff changeset	183 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases" help="Default: 2">
39bac90c773d Uploaded iuc parents: diff changeset	184 <option value="1">1 base</option>
39bac90c773d Uploaded iuc parents: diff changeset	185 <option value="2" selected="true">2 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	186 <option value="3">3 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	187 <option value="4">4 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	188 <option value="5">5 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	189 <option value="6">6 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	190 <option value="7">7 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	191 <option value="8">8 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	192 <option value="9">9 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	193 </param>
39bac90c773d Uploaded iuc parents: diff changeset	194
39bac90c773d Uploaded iuc parents: diff changeset	195 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
39bac90c773d Uploaded iuc parents: diff changeset	196 <option value="no_filter" selected="true">No filter (analyze everything)</option>
39bac90c773d Uploaded iuc parents: diff changeset	197 <option value="-hom">Analyze homozygous sequence changes only</option>
39bac90c773d Uploaded iuc parents: diff changeset	198 <option value="-het">Analyze heterozygous sequence changes only</option>
39bac90c773d Uploaded iuc parents: diff changeset	199 </param>
39bac90c773d Uploaded iuc parents: diff changeset	200
39bac90c773d Uploaded iuc parents: diff changeset	201 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
39bac90c773d Uploaded iuc parents: diff changeset	202 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
39bac90c773d Uploaded iuc parents: diff changeset	203 <option value="-canon">Only use canonical transcripts</option>
39bac90c773d Uploaded iuc parents: diff changeset	204 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
39bac90c773d Uploaded iuc parents: diff changeset	205 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option>
39bac90c773d Uploaded iuc parents: diff changeset	206 <option value="-oicr">Add OICR tag in VCF file</option>
39bac90c773d Uploaded iuc parents: diff changeset	207 <option value="-onlyReg">Only use regulation tracks</option>
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	208 <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>
114f423f99c0 Uploaded iuc parents: 0 diff changeset	209 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option>
114f423f99c0 Uploaded iuc parents: 0 diff changeset	210 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option>
0 39bac90c773d Uploaded iuc parents: diff changeset	211 </param>
39bac90c773d Uploaded iuc parents: diff changeset	212 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
39bac90c773d Uploaded iuc parents: diff changeset	213 <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."/>
39bac90c773d Uploaded iuc parents: diff changeset	214 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
39bac90c773d Uploaded iuc parents: diff changeset	215 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
39bac90c773d Uploaded iuc parents: diff changeset	216 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
39bac90c773d Uploaded iuc parents: diff changeset	217 <option value="-no-intron">Do not show INTRON changes</option>
39bac90c773d Uploaded iuc parents: diff changeset	218 <option value="-no-upstream">Do not show UPSTREAM changes</option>
39bac90c773d Uploaded iuc parents: diff changeset	219 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option>
39bac90c773d Uploaded iuc parents: diff changeset	220 </param>
6 9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	221 <conditional name="filter">
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	222 <param name="specificEffects" type="select" label="Filter out specific Effects">
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	223 <option value="no">No</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	224 <option value="yes">Yes</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	225 </param>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	226 <when value="no"/>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	227 <when value="yes">
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	228 <param name="effects" type="select" display="checkboxes" multiple="true" label="Filter output: do not report these Effects">
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	229 <option value="CDS">CDS (coding_sequence_variant) The variant hits a CDS. MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	230 <option value="CHROMOSOME_LARGE_DELETION">CHROMOSOME_LARGE_DELETION (chromosome) A large parte (over 1%) of the chromosome was deleted. HIGH</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	231 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	232 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	233 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	234 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	235 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	236 <option value="DOWNSTREAM">DOWNSTREAM (downstream_gene_variant) Downstream of a gene (default length: 5K bases) MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	237 <option value="EXON">EXON (exon_variant) The variant hits an exon (from a non-coding transcript) or a retained intron. MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	238 <option value="EXON_DELETED">EXON_DELETED (exon_loss_variant) A deletion removes the whole exon. HIGH</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	239 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	240 <option value="GENE">GENE (gene_variant) The variant hits a gene. MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	241 <option value="INTERGENIC">INTERGENIC (intergenic_region) The variant is in an intergenic region MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	242 <option value="INTERGENIC_CONSERVED">INTERGENIC_CONSERVED (conserved_intergenic_variant) The variant is in a highly conserved intergenic region MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	243 <option value="INTRAGENIC">INTRAGENIC (intragenic_variant) The variant hits a gene, but no transcripts within the gene MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	244 <option value="INTRON">INTRON (intron_variant) Variant hits and intron. Technically, hits no exon in the transcript. MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	245 <option value="INTRON_CONSERVED">INTRON_CONSERVED (conserved_intron_variant) The variant is in a highly conserved intronic region MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	246 <option value="MICRO_RNA">MICRO_RNA (miRNA) Variant affects an miRNA MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	247 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	248 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	249 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	250 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	251 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	252 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	253 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	254 <option value="SPLICE_SITE_BRANCH">SPLICE_SITE_BRANCH (splice_region_variant) A varaint affective putative (Lariat) branch point, located in the intron. LOW</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	255 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	256 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	257 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	258 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	259 <option value="STOP_GAINED">STOP_GAINED (stop_gained) Variant causes a STOP codon e.g.: Cag/Tag, Q/* HIGH</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	260 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	261 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	262 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	263 <option value="TRANSCRIPT">TRANSCRIPT (transcript_variant) The variant hits a transcript. MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	264 <option value="REGULATION">REGULATION (regulatory_region_variant) The variant hits a known regulatory feature (non-coding). MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	265 <option value="UPSTREAM">UPSTREAM (upstream_gene_variant) Upstream of a gene (default length: 5K bases) MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	266 <option value="UTR_3_PRIME">UTR_3_PRIME (3_prime_UTR_variant) Variant hits 3'UTR region MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	267 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	268 <option value="UTR_5_PRIME">UTR_5_PRIME (5_prime_UTR_variant) Variant hits 5'UTR region MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	269 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	270 <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>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	271
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	272 </param>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	273 </when>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	274 </conditional>
0 39bac90c773d Uploaded iuc parents: diff changeset	275
39bac90c773d Uploaded iuc parents: diff changeset	276 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	277 <option value="default" selected="true">Use default (based on input type)</option>
0 39bac90c773d Uploaded iuc parents: diff changeset	278 <option value="-0">Force zero-based positions (both input and output)</option>
39bac90c773d Uploaded iuc parents: diff changeset	279 <option value="-1">Force one-based positions (both input and output)</option>
39bac90c773d Uploaded iuc parents: diff changeset	280 </param>
39bac90c773d Uploaded iuc parents: diff changeset	281 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name">
39bac90c773d Uploaded iuc parents: diff changeset	282 <help>
39bac90c773d Uploaded iuc parents: diff changeset	283 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
39bac90c773d Uploaded iuc parents: diff changeset	284 You can prepend any string you want to the chromosome name.
39bac90c773d Uploaded iuc parents: diff changeset	285 </help>
39bac90c773d Uploaded iuc parents: diff changeset	286 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
39bac90c773d Uploaded iuc parents: diff changeset	287 </param>
39bac90c773d Uploaded iuc parents: diff changeset	288 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
39bac90c773d Uploaded iuc parents: diff changeset	289 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/>
39bac90c773d Uploaded iuc parents: diff changeset	290 </inputs>
39bac90c773d Uploaded iuc parents: diff changeset	291 <outputs>
39bac90c773d Uploaded iuc parents: diff changeset	292 <data format="vcf" name="snpeff_output" >
39bac90c773d Uploaded iuc parents: diff changeset	293 <change_format>
39bac90c773d Uploaded iuc parents: diff changeset	294 <when input="outputConditional.outputFormat" value="txt" format="tabular" />
39bac90c773d Uploaded iuc parents: diff changeset	295 <when input="outputConditional.outputFormat" value="bed" format="bed" />
39bac90c773d Uploaded iuc parents: diff changeset	296 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
39bac90c773d Uploaded iuc parents: diff changeset	297 </change_format>
39bac90c773d Uploaded iuc parents: diff changeset	298 </data>
39bac90c773d Uploaded iuc parents: diff changeset	299 <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats">
39bac90c773d Uploaded iuc parents: diff changeset	300 <filter>generate_stats == True</filter>
39bac90c773d Uploaded iuc parents: diff changeset	301 </data>
39bac90c773d Uploaded iuc parents: diff changeset	302 </outputs>
39bac90c773d Uploaded iuc parents: diff changeset	303 <tests>
39bac90c773d Uploaded iuc parents: diff changeset	304 <!-- Check that an effect was added in out VCF -->
39bac90c773d Uploaded iuc parents: diff changeset	305 <!-- Check for a HTML header indicating that this was successful -->
39bac90c773d Uploaded iuc parents: diff changeset	306 <!--
39bac90c773d Uploaded iuc parents: diff changeset	307 <output name="statsFile">
39bac90c773d Uploaded iuc parents: diff changeset	308 <assert_contents>
39bac90c773d Uploaded iuc parents: diff changeset	309 <has_text text="SnpEff: Variant analysis" />
39bac90c773d Uploaded iuc parents: diff changeset	310 </assert_contents>
39bac90c773d Uploaded iuc parents: diff changeset	311 </output>
5 92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 2 diff changeset	312 -->
0 39bac90c773d Uploaded iuc parents: diff changeset	313 <!-- Setting filterOut throws exception in twilltestcase.py
39bac90c773d Uploaded iuc parents: diff changeset	314 <test>
39bac90c773d Uploaded iuc parents: diff changeset	315 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
39bac90c773d Uploaded iuc parents: diff changeset	316 <param name="inputFormat" value="vcf"/>
39bac90c773d Uploaded iuc parents: diff changeset	317 <param name="outputFormat" value="vcf"/>
39bac90c773d Uploaded iuc parents: diff changeset	318 <param name="genomeSrc" value="named"/>
39bac90c773d Uploaded iuc parents: diff changeset	319 <param name="genome_version" value="testCase"/>
39bac90c773d Uploaded iuc parents: diff changeset	320 <param name="udLength" value="0"/>
39bac90c773d Uploaded iuc parents: diff changeset	321 <param name="filterHomHet" value="no_filter"/>
39bac90c773d Uploaded iuc parents: diff changeset	322 <param name="generate_stats" value="False"/>
39bac90c773d Uploaded iuc parents: diff changeset	323 <param name="filterOut" value="+-no-upstream"/>
39bac90c773d Uploaded iuc parents: diff changeset	324 <output name="snpeff_output">
39bac90c773d Uploaded iuc parents: diff changeset	325 <assert_contents>
39bac90c773d Uploaded iuc parents: diff changeset	326 <has_text text="EFF=" />
39bac90c773d Uploaded iuc parents: diff changeset	327 </assert_contents>
39bac90c773d Uploaded iuc parents: diff changeset	328 </output>
39bac90c773d Uploaded iuc parents: diff changeset	329 </test>
5 92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 2 diff changeset	330 -->
0 39bac90c773d Uploaded iuc parents: diff changeset	331
39bac90c773d Uploaded iuc parents: diff changeset	332 <test>
39bac90c773d Uploaded iuc parents: diff changeset	333 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
39bac90c773d Uploaded iuc parents: diff changeset	334 <param name="inputFormat" value="vcf"/>
39bac90c773d Uploaded iuc parents: diff changeset	335 <param name="outputFormat" value="vcf"/>
39bac90c773d Uploaded iuc parents: diff changeset	336 <param name="genomeSrc" value="named"/>
39bac90c773d Uploaded iuc parents: diff changeset	337 <param name="genome_version" value="testCase"/>
39bac90c773d Uploaded iuc parents: diff changeset	338 <param name="udLength" value="0"/>
39bac90c773d Uploaded iuc parents: diff changeset	339 <param name="filterHomHet" value="+-het"/>
39bac90c773d Uploaded iuc parents: diff changeset	340 <!--
39bac90c773d Uploaded iuc parents: diff changeset	341 <param name="filterOut" value=""/>
39bac90c773d Uploaded iuc parents: diff changeset	342 -->
39bac90c773d Uploaded iuc parents: diff changeset	343 <param name="generate_stats" value="False"/>
39bac90c773d Uploaded iuc parents: diff changeset	344 <output name="snpeff_output">
39bac90c773d Uploaded iuc parents: diff changeset	345 <assert_contents>
39bac90c773d Uploaded iuc parents: diff changeset	346 <!-- Check that NO effects were added since -het is set -->
39bac90c773d Uploaded iuc parents: diff changeset	347 <not_has_text text="EFF=NON_SYNONYMOUS_CODING" />
39bac90c773d Uploaded iuc parents: diff changeset	348 </assert_contents>
39bac90c773d Uploaded iuc parents: diff changeset	349 </output>
39bac90c773d Uploaded iuc parents: diff changeset	350 </test>
39bac90c773d Uploaded iuc parents: diff changeset	351
39bac90c773d Uploaded iuc parents: diff changeset	352 <test>
39bac90c773d Uploaded iuc parents: diff changeset	353 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
39bac90c773d Uploaded iuc parents: diff changeset	354 <param name="inputFormat" value="vcf"/>
39bac90c773d Uploaded iuc parents: diff changeset	355 <param name="outputFormat" value="vcf"/>
39bac90c773d Uploaded iuc parents: diff changeset	356 <param name="genomeSrc" value="named"/>
39bac90c773d Uploaded iuc parents: diff changeset	357 <param name="genome_version" value="testCase"/>
39bac90c773d Uploaded iuc parents: diff changeset	358 <param name="udLength" value="0"/>
39bac90c773d Uploaded iuc parents: diff changeset	359 <param name="filterHomHet" value="no_filter"/>
39bac90c773d Uploaded iuc parents: diff changeset	360 <!--
39bac90c773d Uploaded iuc parents: diff changeset	361 <param name="filterOut" value=""/>
39bac90c773d Uploaded iuc parents: diff changeset	362 -->
39bac90c773d Uploaded iuc parents: diff changeset	363 <param name="generate_stats" value="False"/>
39bac90c773d Uploaded iuc parents: diff changeset	364 <output name="snpeff_output">
39bac90c773d Uploaded iuc parents: diff changeset	365 <assert_contents>
39bac90c773d Uploaded iuc parents: diff changeset	366 <!-- Check that deleletions were evaluated -->
39bac90c773d Uploaded iuc parents: diff changeset	367 <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" />
39bac90c773d Uploaded iuc parents: diff changeset	368 <!-- Check that insertion on last line was NOT evaluated -->
39bac90c773d Uploaded iuc parents: diff changeset	369 <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" />
39bac90c773d Uploaded iuc parents: diff changeset	370 </assert_contents>
39bac90c773d Uploaded iuc parents: diff changeset	371 </output>
39bac90c773d Uploaded iuc parents: diff changeset	372 </test>
39bac90c773d Uploaded iuc parents: diff changeset	373
39bac90c773d Uploaded iuc parents: diff changeset	374 <!-- Check that NO UPSTREAM effect was added -->
39bac90c773d Uploaded iuc parents: diff changeset	375 <!-- Setting filterOut throws exception in twilltestcase.py
39bac90c773d Uploaded iuc parents: diff changeset	376 <test>
39bac90c773d Uploaded iuc parents: diff changeset	377 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
39bac90c773d Uploaded iuc parents: diff changeset	378 <param name="inputFormat" value="vcf"/>
39bac90c773d Uploaded iuc parents: diff changeset	379 <param name="outputFormat" value="vcf"/>
39bac90c773d Uploaded iuc parents: diff changeset	380 <param name="genomeSrc" value="named"/>
39bac90c773d Uploaded iuc parents: diff changeset	381 <param name="genome_version" value="testCase"/>
39bac90c773d Uploaded iuc parents: diff changeset	382 <param name="udLength" value="0"/>
39bac90c773d Uploaded iuc parents: diff changeset	383 <param name="filterHomHet" value="no_filter"/>
39bac90c773d Uploaded iuc parents: diff changeset	384 <param name="filterOut" value="+-no-upstream"/>
39bac90c773d Uploaded iuc parents: diff changeset	385 <param name="generate_stats" value="False"/>
39bac90c773d Uploaded iuc parents: diff changeset	386 <output name="snpeff_output">
39bac90c773d Uploaded iuc parents: diff changeset	387 <assert_contents>
39bac90c773d Uploaded iuc parents: diff changeset	388 <not_has_text text="UPSTREAM" />
39bac90c773d Uploaded iuc parents: diff changeset	389 </assert_contents>
39bac90c773d Uploaded iuc parents: diff changeset	390 </output>
39bac90c773d Uploaded iuc parents: diff changeset	391 </test>
39bac90c773d Uploaded iuc parents: diff changeset	392 -->
39bac90c773d Uploaded iuc parents: diff changeset	393
39bac90c773d Uploaded iuc parents: diff changeset	394 </tests>
39bac90c773d Uploaded iuc parents: diff changeset	395 <help>
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	396
0 39bac90c773d Uploaded iuc parents: diff changeset	397 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
39bac90c773d Uploaded iuc parents: diff changeset	398
39bac90c773d Uploaded iuc parents: diff changeset	399 @EXTERNAL_DOCUMENTATION@
39bac90c773d Uploaded iuc parents: diff changeset	400
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	401 @CITATION_SECTION@
114f423f99c0 Uploaded iuc parents: 0 diff changeset	402
0 39bac90c773d Uploaded iuc parents: diff changeset	403 </help>
39bac90c773d Uploaded iuc parents: diff changeset	404 <expand macro="citations" />
39bac90c773d Uploaded iuc parents: diff changeset	405 </tool>
39bac90c773d Uploaded iuc parents: diff changeset	406

Mercurial > repos > iuc > snpeff

annotate snpEff.xml @ 6:9ec1cb6f760d draft