snpeff: snpEff.xml annotate

annotate snpEff.xml @ 22:bb0797deab78 draft

Uploaded

author	jjohnson
date	Wed, 09 Dec 2015 10:20:13 -0500
parents	c780e3f75b3d
children	924af057bbca

rev	line source
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.0">
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	2 <description>Variant effect and annotation</description>
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	3 <macros>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	4 <import>snpEff_macros.xml</import>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	5 </macros>
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	6 <expand macro="requirements" />
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	7 <expand macro="stdio" />
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	8 <expand macro="version_command" />
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	9 <command>
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	10 <![CDATA[
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	11 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	12 -c \$SNPEFF_JAR_PATH/snpEff.config
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	13 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	14 #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	15 -spliceSiteSize $spliceSiteSize
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	16 #end if
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	17 #if $spliceRegion.setSpliceRegions == 'yes':
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	18 #if $spliceRegion.spliceRegionExonSize and $spliceRegion.spliceRegionExonSize.__str__ != '':
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	19 -spliceRegionExonSize $spliceRegion.spliceRegionExonSize
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	20 #end if
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	21 #if $spliceRegion.spliceRegionIntronMin and $spliceRegion.spliceRegionIntronMin.__str__ != '':
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	22 -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	23 #end if
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	24 #if $spliceRegion.spliceRegionIntronMax and $spliceRegion.spliceRegionIntronMax.__str__ != '':
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	25 -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	26 #end if
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	27 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	28 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	29 $filterHomHet
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	30 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	31 #if $annotations and $annotations.__str__ != '':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	32 #echo " "
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	33 #echo ' '.join($annotations.__str__.split(','))
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	34 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	35 #if $filterOut and $filterOut.__str__ != '':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	36 #echo " "
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	37 #echo ' '.join($filterOut.__str__.split(','))
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	38 #end if
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	39 #if $filter.specificEffects == 'yes' and $filter.effects:
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	40 #for $eff in str($filter.effects).split(','):
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	41 -no $eff
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	42 #end for
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	43 #end if
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	44 #if str( $transcripts ) != 'None':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	45 -onlyTr $transcripts
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	46 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	47 #if str( $intervals ) != 'None': ### fix this for multiple dataset input
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	48 -interval $intervals
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	49 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	50 #if $statsFile:
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	51 -stats $statsFile
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	52 #end if
16 3790e16a0be0 Add datatype: snpeffdbv4 Jim Johnson <jj@umn.edu> parents: 15 diff changeset	53 #if $offset.__str__ != 'default':
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	54 ${offset}
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	55 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	56 #if $chr.__str__.strip() != '':
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	57 -chr "$chr"
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	58 #end if
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	59 $noLog
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	60 #if $snpDb.genomeSrc == 'cached':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	61 -dataDir ${snpDb.genomeVersion.fields.path}
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	62 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	63 #echo " "
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	64 #echo ' '.join($snpDb.extra_annotations.__str__.split(','))
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	65 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	66 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	67 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	68 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	69 $snpDb.genomeVersion
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	70 #elif $snpDb.genomeSrc == 'history':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	71 -dataDir ${snpDb.snpeff_db.extra_files_path}
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	72 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
10 39cb913568ec Do not select any annotations by default Jim Johnson <jj@umn.edu> parents: 9 diff changeset	73 #set xannotations = [' '] + $snpDb.extra_annotations.__str__.split(',')
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	74 #echo " "
10 39cb913568ec Do not select any annotations by default Jim Johnson <jj@umn.edu> parents: 9 diff changeset	75 #echo ' -'.join($xannotations)
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	76 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	77 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	78 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	79 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	80 ${snpDb.snpeff_db.metadata.genome_version}
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	81 #else
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	82 -download
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	83 $snpDb.genome_version
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	84 #end if
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	85 $input > $snpeff_output ;
17 13d81e5226cd Put gene info in Summary Report extra_files_path Jim Johnson <jj@umn.edu> parents: 16 diff changeset	86 #if $statsFile:
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	87 #import os
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	88 #set $genes_file = str($statsFile) + '.genes.txt'
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	89 #set $genes_file_name = os.path.split($genes_file)[-1]
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	90 mkdir $statsFile.files_path;
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	91 mv $genes_file #echo os.path.join($statsFile.files_path, $genes_file_name)#;
17 13d81e5226cd Put gene info in Summary Report extra_files_path Jim Johnson <jj@umn.edu> parents: 16 diff changeset	92 #end if
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	93 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	94 ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]"
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	95 sed -i -e 's/^\#\#SnpEffVersion="$\S*\s$/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	96 #end if
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	97 ]]>
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	98 </command>
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	99 <inputs>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	100 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	101
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	102 <param name="inputFormat" type="select" label="Input format">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	103 <option value="vcf" selected="true">VCF</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	104 <option value="bed">BED (Deprecated)</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	105 </param>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	106
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	107 <conditional name="outputConditional">
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	108 <param name="outputFormat" type="select" label="Output format">
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	109 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	110 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	111 <option value="bed">BED</option>
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	112 <option value="bedAnn">BED annotations</option>
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	113 </param>
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	114 <when value="vcf" />
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	115 <when value="gatk">
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	116 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	117 </when>
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	118 <when value="bed" />
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	119 <when value="bedAnn" />
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	120 </conditional>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	121
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	122 <conditional name="snpDb">
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	123 <param name="genomeSrc" type="select" label="Genome source">
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	124 <option value="cached">Locally installed reference genome</option>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	125 <option value="history">Reference genome from your history</option>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	126 <option value="named">Named on demand</option>
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	127 </param>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	128 <when value="cached">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	129 <param name="genomeVersion" type="select" label="Genome">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	130 <!--GENOME DESCRIPTION-->
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	131 <options from_data_table="snpeffv_genomedb">
21 c780e3f75b3d Filter genome history snpeffdb by snpeff_version Jim Johnson <jj@umn.edu> parents: 19 diff changeset	132 <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/>
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	133 <filter type="unique_value" column="2" />
6 eb394dd65c98 Add mutli-select to data managers from Bjoern, filter unique database options in snpEff_download.xml snpEff.xml Jim Johnson <jj@umn.edu> parents: 5 diff changeset	134 </options>
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	135 </param>
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	136 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
2 6ad9205c1307 Update to SnpEff version 3.3 Jim Johnson <jj@umn.edu> parents: 0 diff changeset	137 <help>These are available for only a few genomes</help>
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	138 <options from_data_table="snpeffv_annotations">
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	139 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
19 2e37b58fc24d Fix some versions Jim Johnson <jj@umn.edu> parents: 18 diff changeset	140 <filter type="unique_value" column="3" />
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	141 </options>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	142 </param>
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	143 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation">
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	144 <help>These are available for only a few genomes</help>
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	145 <options from_data_table="snpeffv_regulationdb">
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	146 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
19 2e37b58fc24d Fix some versions Jim Johnson <jj@umn.edu> parents: 18 diff changeset	147 <filter type="unique_value" column="3" />
2 6ad9205c1307 Update to SnpEff version 3.3 Jim Johnson <jj@umn.edu> parents: 0 diff changeset	148 </options>
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	149 </param>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	150 </when>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	151 <when value="history">
21 c780e3f75b3d Filter genome history snpeffdb by snpeff_version Jim Johnson <jj@umn.edu> parents: 19 diff changeset	152 <param format="snpeffdb" name="snpeff_db" type="data" label="@SNPEFF_VERSION@ Genome Data">
c780e3f75b3d Filter genome history snpeffdb by snpeff_version Jim Johnson <jj@umn.edu> parents: 19 diff changeset	153 <options options_filter_attribute="metadata.snpeff_version" >
c780e3f75b3d Filter genome history snpeffdb by snpeff_version Jim Johnson <jj@umn.edu> parents: 19 diff changeset	154 <filter type="add_value" value="@SNPEFF_VERSION@" />
c780e3f75b3d Filter genome history snpeffdb by snpeff_version Jim Johnson <jj@umn.edu> parents: 19 diff changeset	155 </options>
c780e3f75b3d Filter genome history snpeffdb by snpeff_version Jim Johnson <jj@umn.edu> parents: 19 diff changeset	156 <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>
c780e3f75b3d Filter genome history snpeffdb by snpeff_version Jim Johnson <jj@umn.edu> parents: 19 diff changeset	157 </param>
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	158 <!-- From metadata -->
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	159 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	160 <help>These are available for only a few genomes</help>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	161 <options>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	162 <filter type="data_meta" ref="snpeff_db" key="annotation" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	163 </options>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	164 </param>
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	165 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation">
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	166 <help>These are available for only a few genomes</help>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	167 <options>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	168 <filter type="data_meta" ref="snpeff_db" key="regulation" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	169 </options>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	170 </param>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	171 </when>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	172 <when value="named">
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	173 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	174 <help>@SNPEFF_DATABASE_URL@</help>
16 3790e16a0be0 Add datatype: snpeffdbv4 Jim Johnson <jj@umn.edu> parents: 15 diff changeset	175 <validator type="regex" message="A genome version name is required">\S+</validator>
3790e16a0be0 Add datatype: snpeffdbv4 Jim Johnson <jj@umn.edu> parents: 15 diff changeset	176 </param>
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	177 </when>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	178 </conditional>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	179
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	180 <param name="udLength" type="select" label="Upstream / Downstream length">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	181 <option value="0">No upstream / downstream intervals (0 bases)</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	182 <option value="200">200 bases</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	183 <option value="500">500 bases</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	184 <option value="1000">1000 bases</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	185 <option value="2000">2000 bases</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	186 <option value="5000" selected="true">5000 bases</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	187 <option value="10000">10000 bases</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	188 <option value="20000">20000 bases</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	189 </param>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	190
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	191 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases" help="Default: 2">
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	192 <option value="1">1 base</option>
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	193 <option value="2" selected="true">2 bases</option>
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	194 <option value="3">3 bases</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	195 <option value="4">4 bases</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	196 <option value="5">5 bases</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	197 <option value="6">6 bases</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	198 <option value="7">7 bases</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	199 <option value="8">8 bases</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	200 <option value="9">9 bases</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	201 </param>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	202
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	203 <conditional name="spliceRegion">
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	204 <param name="setSpliceRegions" type="select" label="spliceRegion Settings">
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	205 <option value="no">Use Defaults</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	206 <option value="yes">Set Splice Region Parameters</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	207 </param>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	208 <when value="no"/>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	209 <when value="yes">
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	210 <param name="spliceRegionExonSize" type="integer" value="" min="1" max="10" optional="true" label="Set size for splice site region within exons. Default: 3 bases"/>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	211 <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"/>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	212 <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"/>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	213 </when>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	214 </conditional>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	215
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	216 <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	217 <option value="no_filter" selected="true">No filter (analyze everything)</option>
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	218 <option value="-hom">Analyze homozygous sequence changes only</option>
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	219 <option value="-het">Analyze heterozygous sequence changes only</option>
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	220 </param>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	221
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	222 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	223 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
10 39cb913568ec Do not select any annotations by default Jim Johnson <jj@umn.edu> parents: 9 diff changeset	224 <option value="-canon">Only use canonical transcripts</option>
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	225 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	226 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option>
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	227 <option value="-oicr">Add OICR tag in VCF file</option>
10 39cb913568ec Do not select any annotations by default Jim Johnson <jj@umn.edu> parents: 9 diff changeset	228 <option value="-onlyReg">Only use regulation tracks</option>
12 6d429d880a75 Update for snpeff version 4.0 Jim Johnson <jj@umn.edu> parents: 11 diff changeset	229 <option value="-classic">Use Classic Effect names and amino acid variant annotations (NON_SYNONYMOUS_CODING vs missense_variant and G180R vs p.Gly180Arg/c.538G>C)</option>
6d429d880a75 Update for snpeff version 4.0 Jim Johnson <jj@umn.edu> parents: 11 diff changeset	230 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option>
6d429d880a75 Update for snpeff version 4.0 Jim Johnson <jj@umn.edu> parents: 11 diff changeset	231 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option>
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	232 <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN').</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	233 <option value="-noHgvs">Do not add HGVS annotations.</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	234 <option value="-noLof">Do not add LOF and NMD annotations.</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	235 <option value="-noShiftHgvs">Do not shift variants according to HGVS notation (most 3prime end).</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	236 <option value="-oicr">Add OICR tag in VCF file. Default: false</option>
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	237 </param>
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	238 <!-- -cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples. -->
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	239 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	240 <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."/>
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	241 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	242 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	243 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	244 <option value="-no-intron">Do not show INTRON changes</option>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	245 <option value="-no-upstream">Do not show UPSTREAM changes</option>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	246 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option>
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	247 </param>
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	248 <conditional name="filter">
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	249 <param name="specificEffects" type="select" label="Filter out specific Effects">
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	250 <option value="no">No</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	251 <option value="yes">Yes</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	252 </param>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	253 <when value="no"/>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	254 <when value="yes">
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	255 <param name="effects" type="select" display="checkboxes" multiple="true" label="Filter output: do not report these Effects">
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	256 <option value="CDS">CDS (coding_sequence_variant) The variant hits a CDS. MODIFIER</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	257 <option value="CHROMOSOME_LARGE_DELETION">CHROMOSOME_LARGE_DELETION (chromosome) A large parte (over 1%) of the chromosome was deleted. HIGH</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	258 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	259 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	260 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	261 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	262 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	263 <option value="DOWNSTREAM">DOWNSTREAM (downstream_gene_variant) Downstream of a gene (default length: 5K bases) MODIFIER</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	264 <option value="EXON">EXON (exon_variant) The variant hits an exon (from a non-coding transcript) or a retained intron. MODIFIER</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	265 <option value="EXON_DELETED">EXON_DELETED (exon_loss_variant) A deletion removes the whole exon. HIGH</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	266 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	267 <option value="GENE">GENE (gene_variant) The variant hits a gene. MODIFIER</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	268 <option value="INTERGENIC">INTERGENIC (intergenic_region) The variant is in an intergenic region MODIFIER</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	269 <option value="INTERGENIC_CONSERVED">INTERGENIC_CONSERVED (conserved_intergenic_variant) The variant is in a highly conserved intergenic region MODIFIER</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	270 <option value="INTRAGENIC">INTRAGENIC (intragenic_variant) The variant hits a gene, but no transcripts within the gene MODIFIER</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	271 <option value="INTRON">INTRON (intron_variant) Variant hits and intron. Technically, hits no exon in the transcript. MODIFIER</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	272 <option value="INTRON_CONSERVED">INTRON_CONSERVED (conserved_intron_variant) The variant is in a highly conserved intronic region MODIFIER</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	273 <option value="MICRO_RNA">MICRO_RNA (miRNA) Variant affects an miRNA MODIFIER</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	274 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	275 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	276 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	277 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	278 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	279 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	280 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	281 <option value="SPLICE_SITE_BRANCH">SPLICE_SITE_BRANCH (splice_region_variant) A varaint affective putative (Lariat) branch point, located in the intron. LOW</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	282 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	283 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	284 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	285 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	286 <option value="STOP_GAINED">STOP_GAINED (stop_gained) Variant causes a STOP codon e.g.: Cag/Tag, Q/* HIGH</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	287 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	288 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	289 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	290 <option value="TRANSCRIPT">TRANSCRIPT (transcript_variant) The variant hits a transcript. MODIFIER</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	291 <option value="REGULATION">REGULATION (regulatory_region_variant) The variant hits a known regulatory feature (non-coding). MODIFIER</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	292 <option value="UPSTREAM">UPSTREAM (upstream_gene_variant) Upstream of a gene (default length: 5K bases) MODIFIER</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	293 <option value="UTR_3_PRIME">UTR_3_PRIME (3_prime_UTR_variant) Variant hits 3'UTR region MODIFIER</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	294 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	295 <option value="UTR_5_PRIME">UTR_5_PRIME (5_prime_UTR_variant) Variant hits 5'UTR region MODIFIER</option>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	296 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	297 <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>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	298
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	299 </param>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	300 </when>
bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	301 </conditional>
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	302
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	303 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
16 3790e16a0be0 Add datatype: snpeffdbv4 Jim Johnson <jj@umn.edu> parents: 15 diff changeset	304 <option value="default" selected="true">Use default (based on input type)</option>
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	305 <option value="-0">Force zero-based positions (both input and output)</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	306 <option value="-1">Force one-based positions (both input and output)</option>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	307 </param>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	308 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name">
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	309 <help>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	310 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	311 You can prepend any string you want to the chromosome name.
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	312 </help>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	313 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	314 </param>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	315 <param name="generate_stats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	316 <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Do not report usage statistics to server"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	317 </inputs>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	318 <outputs>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	319 <data format="vcf" name="snpeff_output" >
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	320 <change_format>
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	321 <when input="outputConditional.outputFormat" value="bed" format="bed" />
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	322 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	323 </change_format>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	324 </data>
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	325 <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats">
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	326 <filter>generate_stats == True</filter>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	327 </data>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	328 </outputs>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	329 <tests>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	330 <!-- Check that an effect was added in out VCF -->
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	331 <!-- Check for a HTML header indicating that this was successful -->
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	332 <!--
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	333 <output name="statsFile">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	334 <assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	335 <has_text text="SnpEff: Variant analysis" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	336 </assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	337 </output>
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	338 -->
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	339 <!-- Setting filterOut throws exception in twilltestcase.py
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	340 <test>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	341 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	342 <param name="inputFormat" value="vcf"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	343 <param name="outputFormat" value="vcf"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	344 <param name="genomeSrc" value="named"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	345 <param name="genome_version" value="testCase"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	346 <param name="udLength" value="0"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	347 <param name="filterHomHet" value="no_filter"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	348 <param name="generate_stats" value="False"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	349 <param name="filterOut" value="+-no-upstream"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	350 <output name="snpeff_output">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	351 <assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	352 <has_text text="EFF=" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	353 </assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	354 </output>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	355 </test>
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	356 -->
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	357
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	358 <test>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	359 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	360 <param name="inputFormat" value="vcf"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	361 <param name="outputFormat" value="vcf"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	362 <param name="genomeSrc" value="named"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	363 <param name="genome_version" value="testCase"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	364 <param name="udLength" value="0"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	365 <param name="filterHomHet" value="+-het"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	366 <!--
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	367 <param name="filterOut" value=""/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	368 -->
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	369 <param name="generate_stats" value="False"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	370 <output name="snpeff_output">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	371 <assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	372 <!-- Check that NO effects were added since -het is set -->
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	373 <not_has_text text="EFF=NON_SYNONYMOUS_CODING" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	374 </assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	375 </output>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	376 </test>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	377
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	378 <test>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	379 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	380 <param name="inputFormat" value="vcf"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	381 <param name="outputFormat" value="vcf"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	382 <param name="genomeSrc" value="named"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	383 <param name="genome_version" value="testCase"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	384 <param name="udLength" value="0"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	385 <param name="filterHomHet" value="no_filter"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	386 <!--
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	387 <param name="filterOut" value=""/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	388 -->
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	389 <param name="generate_stats" value="False"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	390 <output name="snpeff_output">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	391 <assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	392 <!-- Check that deleletions were evaluated -->
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	393 <has_text_matching expression="Y\t59030478\t.*EFF=INTERGENIC" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	394 <!-- Check that insertion on last line was NOT evaluated -->
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	395 <has_text_matching expression="Y\t59032947\t.*SF=5\tGT" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	396 </assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	397 </output>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	398 </test>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	399
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	400 <!-- Check that NO UPSTREAM effect was added -->
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	401 <!-- Setting filterOut throws exception in twilltestcase.py
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	402 <test>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	403 <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	404 <param name="inputFormat" value="vcf"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	405 <param name="outputFormat" value="vcf"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	406 <param name="genomeSrc" value="named"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	407 <param name="genome_version" value="testCase"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	408 <param name="udLength" value="0"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	409 <param name="filterHomHet" value="no_filter"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	410 <param name="filterOut" value="+-no-upstream"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	411 <param name="generate_stats" value="False"/>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	412 <output name="snpeff_output">
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	413 <assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	414 <not_has_text text="UPSTREAM" />
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	415 </assert_contents>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	416 </output>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	417 </test>
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	418 -->
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	419
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	420 </tests>
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	421 <help><![CDATA[
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	422
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	423 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	424
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	425 @EXTERNAL_DOCUMENTATION@
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	426
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	427 @CITATION_SECTION@
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	428
22 bb0797deab78 Uploaded jjohnson parents: 21 diff changeset	429 ]]>
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	430 </help>
18 36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	431 <expand macro="citations" />
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	432 </tool>
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	433

Mercurial > repos > jjohnson > snpeff

annotate snpEff.xml @ 22:bb0797deab78 draft