snpeff: snpEff.xml annotate

annotate snpEff.xml @ 21:c780e3f75b3d

Filter genome history snpeffdb by snpeff_version

author	Jim Johnson <jj@umn.edu>
date	Wed, 14 Jan 2015 12:03:21 -0600
parents	2e37b58fc24d
children	bb0797deab78

rev	line source
21 c780e3f75b3d Filter genome history snpeffdb by snpeff_version Jim Johnson <jj@umn.edu> parents: 19 diff changeset	1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.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	2 <description>Variant effect and annotation</description>
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	3 <expand macro="requirements" />
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	4 <macros>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	5 <import>snpEff_macros.xml</import>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	6 </macros>
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	7 <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	8 <![CDATA[
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	9 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	10 -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	11 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	12 #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	13 -spliceSiteSize $spliceSiteSize
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	14 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	15 #if $filterIn and $filterIn.__str__ != 'no_filter':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	16 $filterIn
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	17 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	18 #if $filterHomHet and $filterHomHet.__str__ != 'no_filter':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	19 $filterHomHet
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	20 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	21 #if $annotations and $annotations.__str__ != '':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	22 #echo " "
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	23 #echo ' '.join($annotations.__str__.split(','))
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	24 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	25 #if $filterOut and $filterOut.__str__ != '':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	26 #echo " "
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	27 #echo ' '.join($filterOut.__str__.split(','))
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	28 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	29 #if str( $transcripts ) != 'None':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	30 -onlyTr $transcripts
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	31 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	32 #if str( $intervals ) != 'None': ### fix this for multiple dataset input
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	33 -interval $intervals
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	34 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	35 #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	36 -stats $statsFile
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	37 #end if
16 3790e16a0be0 Add datatype: snpeffdbv4 Jim Johnson <jj@umn.edu> parents: 15 diff changeset	38 #if $offset.__str__ != 'default':
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	39 ${offset}
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	40 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	41 #if $chr.__str__.strip() != '':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	42 -chr "$chr"
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	43 #end if
16 3790e16a0be0 Add datatype: snpeffdbv4 Jim Johnson <jj@umn.edu> parents: 15 diff changeset	44 $noLog
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	45 #if $snpDb.genomeSrc == 'cached':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	46 -dataDir ${snpDb.genomeVersion.fields.path}
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	47 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	48 #echo " "
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	49 #echo ' '.join($snpDb.extra_annotations.__str__.split(','))
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	50 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	51 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	52 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	53 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	54 $snpDb.genomeVersion
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	55 #elif $snpDb.genomeSrc == 'history':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	56 -dataDir ${snpDb.snpeff_db.extra_files_path}
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	57 #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	58 #set xannotations = [' '] + $snpDb.extra_annotations.__str__.split(',')
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	59 #echo " "
10 39cb913568ec Do not select any annotations by default Jim Johnson <jj@umn.edu> parents: 9 diff changeset	60 #echo ' -'.join($xannotations)
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	61 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	62 #if $snpDb.regulation and $snpDb.regulation.__str__ != '':
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	63 -reg #echo ' -reg '.join($snpDb.regulation.__str__.split(','))#
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	64 #end if
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	65 ${snpDb.snpeff_db.metadata.genome_version}
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	66 #else
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	67 -download
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	68 $snpDb.genome_version
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	69 #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	70 $input > $snpeff_output ;
17 13d81e5226cd Put gene info in Summary Report extra_files_path Jim Johnson <jj@umn.edu> parents: 16 diff changeset	71 #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	72 #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	73 #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	74 #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	75 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	76 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	77 #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	78 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	79 ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]"
36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file Jim Johnson <jj@umn.edu> parents: 17 diff changeset	80 sed -i 's/^\#\#SnpEffVersion="$\S*\s$/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output
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	81 #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	82 ]]>
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	83 </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	84 <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	85 <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>
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 <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	88 <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	89 <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	90 <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	91 <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	92 </param>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	93
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	94 <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	95 <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	96 <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	97 <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	98 <option value="txt">Tabular</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	99 <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	100 <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	101 </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	102 <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	103 <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	104 <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	105 </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	106 <when value="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	107 <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	108 <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	109 </conditional>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	110
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 <conditional name="snpDb">
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	112 <param name="genomeSrc" type="select" label="Genome source">
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	113 <option value="cached">Locally installed reference genome</option>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	114 <option value="history">Reference genome from your history</option>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	115 <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	116 </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	117 <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	118 <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	119 <!--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	120 <options from_data_table="snpeffv_genomedb">
21 c780e3f75b3d Filter genome history snpeffdb by snpeff_version Jim Johnson <jj@umn.edu> parents: 19 diff changeset	121 <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	122 <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	123 </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	124 </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	125 <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	126 <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	127 <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	128 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
19 2e37b58fc24d Fix some versions Jim Johnson <jj@umn.edu> parents: 18 diff changeset	129 <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	130 </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	131 </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	132 <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	133 <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	134 <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	135 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
19 2e37b58fc24d Fix some versions Jim Johnson <jj@umn.edu> parents: 18 diff changeset	136 <filter type="unique_value" column="3" />
2 6ad9205c1307 Update to SnpEff version 3.3 Jim Johnson <jj@umn.edu> parents: 0 diff changeset	137 </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	138 </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	139 </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	140 <when value="history">
21 c780e3f75b3d Filter genome history snpeffdb by snpeff_version Jim Johnson <jj@umn.edu> parents: 19 diff changeset	141 <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	142 <options options_filter_attribute="metadata.snpeff_version" >
c780e3f75b3d Filter genome history snpeffdb by snpeff_version Jim Johnson <jj@umn.edu> parents: 19 diff changeset	143 <filter type="add_value" value="@SNPEFF_VERSION@" />
c780e3f75b3d Filter genome history snpeffdb by snpeff_version Jim Johnson <jj@umn.edu> parents: 19 diff changeset	144 </options>
c780e3f75b3d Filter genome history snpeffdb by snpeff_version Jim Johnson <jj@umn.edu> parents: 19 diff changeset	145 <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	146 </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	147 <!-- 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	148 <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	149 <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	150 <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	151 <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	152 </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	153 </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	154 <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	155 <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	156 <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	157 <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	158 </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	159 </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	160 </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	161 <when value="named">
16 3790e16a0be0 Add datatype: snpeffdbv4 Jim Johnson <jj@umn.edu> parents: 15 diff changeset	162 <param name="genome_version" type="text" size="40" 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	163 <help>@SNPEFF_DATABASE_URL@</help>
16 3790e16a0be0 Add datatype: snpeffdbv4 Jim Johnson <jj@umn.edu> parents: 15 diff changeset	164 <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	165 </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	166 </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	167 </conditional>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	168
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	169 <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	170 <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	171 <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	172 <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	173 <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	174 <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	175 <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	176 <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	177 <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	178 </param>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	179
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	180 <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	181 <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	182 <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	183 <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	184 <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	185 <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	186 <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	187 <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	188 <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	189 <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	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="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	193 <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	194 <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	195 <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	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
8952990fcab9 Update 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 <!-- 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	199 <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	200 <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	201 <option value="-del">Analyze deletions 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	202 <option value="-ins">Analyze insertions 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	203 <option value="-mnp">Only MNPs (multiple nucleotide polymorphisms)</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	204 <option value="-snp">Only SNPs (single nucleotide polymorphisms)</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	205 </param>
2 6ad9205c1307 Update to SnpEff version 3.3 Jim Johnson <jj@umn.edu> parents: 0 diff changeset	206
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	207 <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	208 <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	209 <option value="-canon">Only use canonical transcripts</option>
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	210 <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	211 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option>
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	212 <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	213 <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	214 <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	215 <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	216 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</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	217 </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	218 <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/>
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	219 <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	220 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	221 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	222 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	223 <option value="-no-intron">Do not show INTRON changes</option>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	224 <option value="-no-upstream">Do not show UPSTREAM changes</option>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	225 <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	226 </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	227
8952990fcab9 Update 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 <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	229 <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	230 <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	231 <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	232 </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	233 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name">
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	234 <help>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	235 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	236 You can prepend any string you want to the chromosome name.
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	237 </help>
0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	238 <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	239 </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	240 <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	241 <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	242 </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	243 <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	244 <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	245 <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	246 <when input="outputConditional.outputFormat" value="txt" format="tabular" />
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	247 <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	248 <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	249 </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	250 </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	251 <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	252 <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	253 </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	254 </outputs>
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	255 <expand macro="stdio" />
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 <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	257 <!-- 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	258 <!-- 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	259 <!--
8952990fcab9 Update 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 <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	261 <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	262 <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	263 </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	264 </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	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 <!-- 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	267 <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	268 <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	269 <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	270 <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	271 <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	272 <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	273 <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	274 <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	275 <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	276 <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	277 <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	278 <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	279 <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	280 <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	281 </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	282 </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	283 </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	284 -->
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	285
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	286 <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	287 <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	288 <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	289 <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	290 <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	291 <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	292 <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	293 <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	294 <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	295 <!--
8952990fcab9 Update 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 <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	297 -->
8952990fcab9 Update 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 <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	299 <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	300 <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	301 <!-- 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	302 <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	303 </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	304 </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	305 </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	306
8952990fcab9 Update 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 <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	308 <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	309 <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	310 <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	311 <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	312 <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	313 <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	314 <param name="filterHomHet" value="no_filter"/>
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	315 <param name="filterIn" value="+-del"/>
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	316 <!--
8952990fcab9 Update 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 <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	318 -->
8952990fcab9 Update 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 <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	320 <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	321 <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	322 <!-- 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	323 <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	324 <!-- 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	325 <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	326 </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	327 </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	328 </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	329
8952990fcab9 Update 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 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	331 <!-- 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	332 <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	333 <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	334 <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	335 <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	336 <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	337 <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	338 <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	339 <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	340 <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	341 <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	342 <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	343 <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	344 <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	345 <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	346 </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	347 </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	348 </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	349 -->
8952990fcab9 Update 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
8952990fcab9 Update 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 </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	352 <help>
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	353
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	354 This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	355
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	356 @EXTERNAL_DOCUMENTATION@
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	357
7 0ad9733e22a4 Uploaded bgruening parents: 6 diff changeset	358 @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	359
8952990fcab9 Update 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 </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	361 <expand macro="citations" />
0 e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	362 </tool>
e1d9f6a0ad53 Uploaded jjohnson parents: diff changeset	363

Mercurial > repos > jjohnson > snpeff

annotate snpEff.xml @ 21:c780e3f75b3d