snpeff: snpEff.xml annotate

annotate snpEff.xml @ 6:eb394dd65c98

Add mutli-select to data managers from Bjoern, filter unique database options in snpEff_download.xml snpEff.xml

author	Jim Johnson <jj@umn.edu>
date	Thu, 28 Nov 2013 08:16:11 -0600
parents	8952990fcab9
children	0ad9733e22a4

rev	line source
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	1 <tool id="snpEff" name="SnpEff" version="3.4">
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>
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	3 <requirements>
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	4 <requirement type="package" version="3.4">snpEff</requirement>
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	5 </requirements>
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	6 <command>
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	7 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar 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	8 -c \$SNPEFF_JAR_PATH/snpEff.config
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 -i $inputFormat -o $outputFormat -upDownStreamLen $udLength
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	10 #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	11 -spliceSiteSize $spliceSiteSize
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	12 #end if
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	13 #if $filterIn and $filterIn.__str__ != 'no_filter':
2 6ad9205c1307 Update to SnpEff version 3.3 Jim Johnson <jj@umn.edu> parents: 0 diff changeset	14 $filterIn
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	15 #end if
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	16 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
2 6ad9205c1307 Update to SnpEff version 3.3 Jim Johnson <jj@umn.edu> parents: 0 diff changeset	17 $filterHomHet
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	18 #end if
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	19 #if $annotations and $annotations.__str__ != '':
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	20 #echo " "
2 6ad9205c1307 Update to SnpEff version 3.3 Jim Johnson <jj@umn.edu> parents: 0 diff changeset	21 #echo ' '.join($annotations.__str__.split(','))
6ad9205c1307 Update to SnpEff version 3.3 Jim Johnson <jj@umn.edu> parents: 0 diff changeset	22 #end if
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	23 #if $filterOut and $filterOut.__str__ != '':
5 8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	24 #echo " "
2 6ad9205c1307 Update to SnpEff version 3.3 Jim Johnson <jj@umn.edu> parents: 0 diff changeset	25 #echo ' '.join($filterOut.__str__.split(','))
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	26 #end if
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	27 #if str( $transcripts ) != 'None':
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	28 -onlyTr $transcripts
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	29 #end if
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	30 #if str( $intervals ) != 'None': ### fix this for multiple dataset input
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	31 -interval $intervals
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	32 #end if
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	33 #if $statsFile:
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	34 -stats $statsFile
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	35 #end if
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	36 #if $offset.__str__ != '':
2 6ad9205c1307 Update to SnpEff version 3.3 Jim Johnson <jj@umn.edu> parents: 0 diff changeset	37 ${offset}
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	38 #end if
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	39 #if $chr.__str__.strip() != '':
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	40 -chr "$chr"
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	41 #end if
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	42 $noLog
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	43 #if $snpDb.genomeSrc == '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	44 -dataDir ${snpDb.genomeVersion.fields.path}
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	45 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	46 #echo " "
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	47 #echo ' '.join($snpDb.extra_annotations.__str__.split(','))
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	48 #end if
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	49 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	50 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
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	51 #end if
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	52 $snpDb.genomeVersion
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	53 #elif $snpDb.genomeSrc == 'history':
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	54 -dataDir ${snpDb.snpeff_db.extra_files_path}
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	55 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
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	56 #set annotations = [' '] + $snpDb.extra_annotations.__str__.split(',')
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	57 #echo " "
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	58 #echo ' -'.join($annotations)
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	59 #end if
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	60 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
8952990fcab9 Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases Jim Johnson <jj@umn.edu> parents: 2 diff changeset	61 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
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	62 #end if
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	63 ${snpDb.snpeff_db.metadata.genome_version}
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	64 #else
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	65 -download
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	66 $snpDb.genome_version
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	67 #end if
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	68 $input > $snpeff_output
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	69 </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	70 <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	71 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	72
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	73 <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	74 <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	75 <option value="txt">Tabular (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	76 <option value="pileup">Pileup (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	77 <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	78 </param>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	79
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	80 <param name="outputFormat" type="select" label="Output 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	81 <option value="vcf" selected="true">VCF (only if input is 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	82 <option value="txt">Tabular</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	83 <option value="bed">BED</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	84 <option value="bedAnn">BED Annotations</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	85 </param>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	86
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	87 <conditional name="snpDb">
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	88 <param name="genomeSrc" type="select" label="">
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	89 <option value="cached">Locally cached</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	90 <option value="history">history</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	91 <option value="named">named on demand</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	92 </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	93 <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	94 <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	95 <!--GENOME DESCRIPTION-->
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	96 <options from_data_table="snpeff_genomedb">
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	97 <filter type="unique_value" column="0" />
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	98 </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	99 </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	100 <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	101 <help>These are available for only a few genomes</help>
6ad9205c1307 Update to SnpEff version 3.3 Jim Johnson <jj@umn.edu> parents: 0 diff changeset	102 <options from_data_table="snpeff_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	103 <filter type="param_value" ref="genomeVersion" key="genome" column="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	104 </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	105 </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	106 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory 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	107 <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	108 <options from_data_table="snpeff_regulationdb">
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	109 <filter type="param_value" ref="genomeVersion" key="genome" column="0" />
2 6ad9205c1307 Update to SnpEff version 3.3 Jim Johnson <jj@umn.edu> parents: 0 diff changeset	110 </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	111 </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	112 </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	113 <when value="history">
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	114 <param format="snpeffdb" name="snpeff_db" type="data" label="SnpEff Genome Version 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	115 <!-- From metadata -->
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	116 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations">
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	117 <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	118 <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	119 <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	120 </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	121 </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	122 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory 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	123 <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	124 <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	125 <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	126 </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	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>
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 <when 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	130 <param name="genome_version" type="text" value="GRCh37.68" label="Snpff Version Name"/>
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	131 </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	132 </conditional>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	133
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	134 <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	135 <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	136 <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	137 <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	138 <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	139 <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	140 <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	141 <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	142 <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	143 </param>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	144
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	145 <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases. Default: 2">
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	146 <option value="1">1 base</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	147 <option value="2">2 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	148 <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	149 <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	150 <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	151 <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	152 <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	153 <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	154 <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	155 </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	156
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	157 <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	158 <option value="no_filter" selected="true">No filter (analyze everything)</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	159 <option value="-hom">Analyze homozygous sequence changes only </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	160 <option value="-het">Analyze heterozygous sequence changes only </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	161 </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	162
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 <!-- The tool testing code can not handle select,radio,check boxes values that start with '-', so the '-' is added in the command generation -->
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 name="filterIn" type="select" display="radio" label="Filter sequence 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	165 <option value="no_filter" selected="true">No filter (analyze everything)</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	166 <option value="-del">Analyze deletions only </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	167 <option value="-ins">Analyze insertions only </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	168 <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms) </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	169 <option value="-snp">Only SNPs (single nucleotide polymorphisms) </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	170 </param>
2 6ad9205c1307 Update to SnpEff version 3.3 Jim Johnson <jj@umn.edu> parents: 0 diff changeset	171
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	172 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation 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	173 <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline). Default: false</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	174 <option value="-canon">Only use canonical transcripts.</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	175 <option value="-geneId">Use gene ID instead of gene name (VCF output). Default: false</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	176 <option value="-hgvs">Use HGVS annotations for amino acid sub-field. Default: false</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	177 <option value="-lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.</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	178 <option value="-oicr">Add OICR tag in VCF file. Default: false</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	179 <option value="-onlyReg">Only use regulation tracks.</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	180 <option value="-sequenceOntolgy">Use Sequence Ontolgy terms. Default: false</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	181 </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	182 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for 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	183 <param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file. Format: One transcript ID per line."/>
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 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter 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	185 <option value="-no-downstream">Do not show DOWNSTREAM changes </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="-no-intergenic">Do not show INTERGENIC changes </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="-no-intron">Do not show INTRON changes </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="-no-upstream">Do not show UPSTREAM changes </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 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </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	190 </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	191
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 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
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	193 <option value="" selected="true">Use default (based on input type)</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	194 <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	195 <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	196 </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	197 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name">
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 <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	199 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
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 You can prepend any string you want to the chromosome name."
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 </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	202 <validator type="regex" message="No whitespace allows">^\S*$</validator>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	203
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	204 </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	205 <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	206 <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	207 </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	208 <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	209 <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	210 <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	211 <when input="outputFormat" value="vcf" format="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	212 <when input="outputFormat" value="txt" format="tabular" />
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	213 <when input="outputFormat" value="bed" format="bed" />
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	214 <when input="outputFormat" value="bedAnn" format="bed" />
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	215 </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	216 </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	217
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	218 <data format="html" 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	219 <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	220 </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	221 </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	222 <stdio>
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	223 <exit_code range="1:" level="fatal" description="Error" />
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	224 <exit_code range="-1" level="fatal" description="Error: Cannot open file" />
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	225 </stdio>
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	226 <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	227 <!-- 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	228 <!-- 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	229 <!--
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	230 <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	231 <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	232 <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	233 </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	234 </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	235 -->
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	236 <!-- 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	237 <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	238 <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	239 <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	240 <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	241 <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	242 <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	243 <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	244 <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	245 <param name="filterIn" 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	246 <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	247 <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	248 <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	249 <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	250 <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	251 </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	252 </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	253 </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	254 -->
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	255
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	256 <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	257 <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	258 <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	259 <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	260 <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	261 <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	262 <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	263 <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	264 <param name="filterIn" 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	265 <!--
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	266 <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	267 -->
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	268 <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	269 <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	270 <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	271 <!-- 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	272 <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	273 </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	274 </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	275 </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	276
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	277 <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	278 <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	279 <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	280 <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	281 <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	282 <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	283 <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	284 <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	285 <param name="filterIn" value="del"/>
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	286 <!--
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	287 <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	288 -->
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	289 <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	290 <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	291 <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	292 <!-- 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	293 <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	294 <!-- 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	295 <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	296 </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	297 </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	298 </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	299
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	300 <!-- 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	301 <!-- 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	302 <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	303 <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	304 <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	305 <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	306 <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	307 <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	308 <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	309 <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	310 <param name="filterIn" 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	311 <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	312 <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	313 <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	314 <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	315 <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	316 </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	317 </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	318 </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	319 -->
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
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	321 </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	322 <help>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	323
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	324 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	325
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	326 For details about this tool, please go to http://snpEff.sourceforge.net
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	327
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	328 SnpEff citation:
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 "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
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
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 SnpSift citation:
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 "Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
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
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 </help>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	335 </tool>
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	336

Mercurial > repos > jjohnson > snpeff

annotate snpEff.xml @ 6:eb394dd65c98