snpeff: snpEff.xml annotate

annotate snpEff.xml @ 30:0c8a8cd9dd5b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd

author	iuc
date	Sat, 28 Sep 2024 16:27:42 +0000
parents	4c790901c495
children	b7029a54f73e

rev	line source
30 0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	1 <tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy2">
14 a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	2 <description> annotate variants</description>
0 39bac90c773d Uploaded iuc parents: diff changeset	3 <macros>
39bac90c773d Uploaded iuc parents: diff changeset	4 <import>snpEff_macros.xml</import>
39bac90c773d Uploaded iuc parents: diff changeset	5 </macros>
14 a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	6 <requirements>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	7 <expand macro="requirement" />
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	8 </requirements>
5 92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 2 diff changeset	9 <expand macro="stdio" />
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	10 <expand macro="version_command" />
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	11 <command><![CDATA[
30 0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	12 #if $intervals
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	13 ln -s '${intervals}' intervals.bed &&
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	14 #end if
21 9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	15 snpEff @JAVA_OPTIONS@ eff
0 39bac90c773d Uploaded iuc parents: diff changeset	16 -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	17 #if $spliceSiteSize and str($spliceSiteSize) != '':
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	18 -spliceSiteSize "$spliceSiteSize"
0 39bac90c773d Uploaded iuc parents: diff changeset	19 #end if
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	20 #if $spliceRegion.setSpliceRegions == 'yes':
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	21 #if str($spliceRegion.spliceRegionExonSize)
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	22 -spliceRegionExonSize $spliceRegion.spliceRegionExonSize
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	23 #end if
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	24 #if str($spliceRegion.spliceRegionIntronMin)
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	25 -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	26 #end if
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	27 #if str($spliceRegion.spliceRegionIntronMax)
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	28 -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	29 #end if
0 39bac90c773d Uploaded iuc parents: diff changeset	30 #end if
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	31 #if $annotations and str($annotations) != '':
0 39bac90c773d Uploaded iuc parents: diff changeset	32 #echo " "
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	33 #echo ' '.join(str($annotations).split(','))
0 39bac90c773d Uploaded iuc parents: diff changeset	34 #end if
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	35 #if $filterOut and str($filterOut) != '':
0 39bac90c773d Uploaded iuc parents: diff changeset	36 #echo " "
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	37 #echo ' '.join(str($filterOut).split(','))
0 39bac90c773d Uploaded iuc parents: diff changeset	38 #end if
6 9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	39 #if $filter.specificEffects == 'yes' and $filter.effects:
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	40 #for $eff in str($filter.effects).split(','):
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	41 -no $eff
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	42 #end for
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	43 #end if
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	44 #if $transcripts
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	45 -onlyTr '$transcripts'
0 39bac90c773d Uploaded iuc parents: diff changeset	46 #end if
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	47 #if $intervals ### fix this for multiple dataset input
30 0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	48 -interval intervals.bed
0 39bac90c773d Uploaded iuc parents: diff changeset	49 #end if
39bac90c773d Uploaded iuc parents: diff changeset	50 #if $statsFile:
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	51 -stats '$statsFile'
0 39bac90c773d Uploaded iuc parents: diff changeset	52 #end if
18 a9b0163b9fab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 16 diff changeset	53 #if $csvStats:
a9b0163b9fab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 16 diff changeset	54 -csvStats '$csvFile'
a9b0163b9fab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 16 diff changeset	55 #end if
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	56 #if str($offset) != 'default':
5 92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 2 diff changeset	57 ${offset}
0 39bac90c773d Uploaded iuc parents: diff changeset	58 #end if
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	59 #if str($chr).strip() != '':
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	60 -chr '$chr'
0 39bac90c773d Uploaded iuc parents: diff changeset	61 #end if
5 92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 2 diff changeset	62 $noLog
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	63 ## Regulation names can include parentheses: H3K4me3-MSC_(VB)_enriched_sites
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	64 ## Enclose them in in single and double quotes, as the conda snpEff bash script will remove outer quotes
0 39bac90c773d Uploaded iuc parents: diff changeset	65 #if $snpDb.genomeSrc == 'cached':
39bac90c773d Uploaded iuc parents: diff changeset	66 -dataDir ${snpDb.genomeVersion.fields.path}
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	67 #if $snpDb.reg_section.regulation and str($snpDb.reg_section.regulation) != '':
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	68 #set $regs = [x for x in str($snpDb.reg_section.regulation).split(',')]
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	69 #for reg in $regs:
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	70 -reg '"${reg}"'
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	71 #end for
0 39bac90c773d Uploaded iuc parents: diff changeset	72 #end if
39bac90c773d Uploaded iuc parents: diff changeset	73 $snpDb.genomeVersion
39bac90c773d Uploaded iuc parents: diff changeset	74 #elif $snpDb.genomeSrc == 'history':
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	75 -dataDir '${snpDb.snpeff_db.extra_files_path}'
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	76 #if $snpDb.reg_section.regulation and str($snpDb.reg_section.regulation) != '':
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	77 #set $regs = [x for x in str($snpDb.reg_section.regulation).split(',')]
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	78 #for reg in $regs:
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	79 -reg '"${reg}"'
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	80 #end for
0 39bac90c773d Uploaded iuc parents: diff changeset	81 #end if
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	82 '${snpDb.snpeff_db.metadata.genome_version}'
14 a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	83 #elif $snpDb.genomeSrc == 'custom':
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	84 -dataDir '${snpDb.snpeff_db.extra_files_path}'
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	85 -configOption '${snpDb.snpeff_db.metadata.genome_version}'.genome='${snpDb.snpeff_db.metadata.genome_version}'
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	86 -configOption '${snpDb.snpeff_db.metadata.genome_version}'.codonTable='${snpDb.codon_table}'
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	87 '${snpDb.snpeff_db.metadata.genome_version}'
5 92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 2 diff changeset	88 #else
24 4c790901c495 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa iuc parents: 21 diff changeset	89 -dataDir "\$PWD/temp"
0 39bac90c773d Uploaded iuc parents: diff changeset	90 -download
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	91 '$snpDb.genome_version'
0 39bac90c773d Uploaded iuc parents: diff changeset	92 #end if
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	93 '$input' > '$snpeff_output'
0 39bac90c773d Uploaded iuc parents: diff changeset	94 #if $statsFile:
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	95 &&
0 39bac90c773d Uploaded iuc parents: diff changeset	96 #import os
18 a9b0163b9fab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 16 diff changeset	97 #if $csvStats:
a9b0163b9fab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 16 diff changeset	98 #set $genes_file = str($csvFile) + '.genes.txt'
a9b0163b9fab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 16 diff changeset	99 #else
a9b0163b9fab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 16 diff changeset	100 #set $genes_file = str($statsFile) + '.genes.txt'
a9b0163b9fab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 16 diff changeset	101 #end if
0 39bac90c773d Uploaded iuc parents: diff changeset	102 #set $genes_file_name = os.path.split($genes_file)[-1]
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	103 mkdir '$statsFile.files_path' &&
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	104 mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#'
0 39bac90c773d Uploaded iuc parents: diff changeset	105 #end if
39bac90c773d Uploaded iuc parents: diff changeset	106 #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	107 &&
0 39bac90c773d Uploaded iuc parents: diff changeset	108 ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]"
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	109 sed -i.bak -e 's/^\#\#SnpEffVersion="$\S*\s$/\#\#SnpEffVersion="2.0.5 - real is \1/' '$snpeff_output'
0 39bac90c773d Uploaded iuc parents: diff changeset	110 #end if
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	111 ]]></command>
0 39bac90c773d Uploaded iuc parents: diff changeset	112 <inputs>
14 a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	113 <param name="input" type="data" format="vcf,bed" label="Sequence changes (SNPs, MNPs, InDels)"/>
0 39bac90c773d Uploaded iuc parents: diff changeset	114
39bac90c773d Uploaded iuc parents: diff changeset	115 <param name="inputFormat" type="select" label="Input format">
39bac90c773d Uploaded iuc parents: diff changeset	116 <option value="vcf" selected="true">VCF</option>
39bac90c773d Uploaded iuc parents: diff changeset	117 <option value="bed">BED (Deprecated)</option>
39bac90c773d Uploaded iuc parents: diff changeset	118 </param>
39bac90c773d Uploaded iuc parents: diff changeset	119
39bac90c773d Uploaded iuc parents: diff changeset	120 <conditional name="outputConditional">
39bac90c773d Uploaded iuc parents: diff changeset	121 <param name="outputFormat" type="select" label="Output format">
39bac90c773d Uploaded iuc parents: diff changeset	122 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
39bac90c773d Uploaded iuc parents: diff changeset	123 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
39bac90c773d Uploaded iuc parents: diff changeset	124 <option value="bed">BED</option>
39bac90c773d Uploaded iuc parents: diff changeset	125 <option value="bedAnn">BED annotations</option>
39bac90c773d Uploaded iuc parents: diff changeset	126 </param>
39bac90c773d Uploaded iuc parents: diff changeset	127 <when value="vcf" />
39bac90c773d Uploaded iuc parents: diff changeset	128 <when value="gatk">
39bac90c773d Uploaded iuc parents: diff changeset	129 <param name="gatk_v1" type="boolean" checked="true" label="Compatible with GATK 1.x" />
39bac90c773d Uploaded iuc parents: diff changeset	130 </when>
39bac90c773d Uploaded iuc parents: diff changeset	131 <when value="bed" />
39bac90c773d Uploaded iuc parents: diff changeset	132 <when value="bedAnn" />
39bac90c773d Uploaded iuc parents: diff changeset	133 </conditional>
18 a9b0163b9fab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 16 diff changeset	134 <param name="csvStats" type="boolean" truevalue="-csvStats" falsevalue="" checked="false" label="Create CSV report, useful for downstream analysis (-csvStats)" />
0 39bac90c773d Uploaded iuc parents: diff changeset	135 <conditional name="snpDb">
39bac90c773d Uploaded iuc parents: diff changeset	136 <param name="genomeSrc" type="select" label="Genome source">
14 a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	137 <!-- These options are referenced in the help section of SnpEff download tool. If you change them, change help of SnpEff download as well -->
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	138 <option value="cached">Locally installed snpEff database</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	139 <option value="history">Downloaded snpEff database in your history</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	140 <option value="named">Download on demand</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	141 <option value="custom">Custom snpEff database in your history</option>
0 39bac90c773d Uploaded iuc parents: diff changeset	142 </param>
39bac90c773d Uploaded iuc parents: diff changeset	143 <when value="cached">
39bac90c773d Uploaded iuc parents: diff changeset	144 <param name="genomeVersion" type="select" label="Genome">
39bac90c773d Uploaded iuc parents: diff changeset	145 <!--GENOME DESCRIPTION-->
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	146 <options from_data_table="snpeffv_genomedb">
21 9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	147 <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/>
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	148 <filter type="unique_value" column="2" />
0 39bac90c773d Uploaded iuc parents: diff changeset	149 </options>
39bac90c773d Uploaded iuc parents: diff changeset	150 </param>
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	151 <section name="reg_section" expanded="false" title="Regulation options">
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	152 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes">
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	153 <options from_data_table="snpeffv_regulationdb">
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	154 <filter type="param_value" ref="genomeVersion" key="genome" column="2" />
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	155 <filter type="unique_value" column="3" />
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	156 </options>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	157 </param>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	158 </section>
0 39bac90c773d Uploaded iuc parents: diff changeset	159 </when>
39bac90c773d Uploaded iuc parents: diff changeset	160 <when value="history">
21 9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	161 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	162 <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>
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	163 </param>
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	164 <section name="reg_section" expanded="false" title="Regulation options">
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	165 <!-- From metadata -->
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	166 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes">
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	167 <options>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	168 <filter type="data_meta" ref="snpeff_db" key="regulation" />
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	169 </options>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	170 </param>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	171 </section>
0 39bac90c773d Uploaded iuc parents: diff changeset	172 </when>
39bac90c773d Uploaded iuc parents: diff changeset	173 <when value="named">
24 4c790901c495 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa iuc parents: 21 diff changeset	174 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)">
21 9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	175 <help>@SNPEFF_DATABASE_URL@</help>
9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	176 <validator type="empty_field" message="A genome version name is required" />
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	177 </param>
0 39bac90c773d Uploaded iuc parents: diff changeset	178 </when>
14 a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	179 <when value="custom">
21 9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	180 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	181 <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>
14 a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	182 </param>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	183 <param name="codon_table" type="select" label="Select genetic code for this sequence" help="If this sequence uses non-standard genetic code, select one from these options">
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	184 <option selected="true" value="Standard">Standard</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	185 <option value="Vertebrate_Mitochondrial">Vertebrate_Mitochondrial</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	186 <option value="Yeast_Mitochondrial">Yeast_Mitochondrial</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	187 <option value="Mold_Mitochondrial">Mold_Mitochondrial</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	188 <option value="Protozoan_Mitochondrial">Protozoan_Mitochondrial</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	189 <option value="Coelenterate">Coelenterate</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	190 <option value="Mitochondrial">Mitochondrial</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	191 <option value="Mycoplasma">Mycoplasma</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	192 <option value="Spiroplasma">Spiroplasma</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	193 <option value="Invertebrate_Mitochondrial">Invertebrate_Mitochondrial</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	194 <option value="Ciliate_Nuclear">Ciliate_Nuclear</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	195 <option value="Dasycladacean_Nuclear">Dasycladacean_Nuclear</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	196 <option value="Hexamita_Nuclear">Hexamita_Nuclear</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	197 <option value="Echinoderm_Mitochondrial">Echinoderm_Mitochondrial</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	198 <option value="Flatworm_Mitochondrial">Flatworm_Mitochondrial</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	199 <option value="Euplotid_Nuclear">Euplotid_Nuclear</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	200 <option value="Bacterial_and_Plant_Plastid">Bacterial_and_Plant_Plastid</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	201 <option value="Alternative_Yeast_Nuclear">Alternative_Yeast_Nuclear</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	202 <option value="Ascidian_Mitochondrial">Ascidian_Mitochondrial</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	203 <option value="Alternative_Flatworm_Mitochondrial">Alternative_Flatworm_Mitochondrial</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	204 <option value="Blepharisma_Macronuclear">Blepharisma_Macronuclear</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	205 <option value="Chlorophycean_Mitochondrial">Chlorophycean_Mitochondrial</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	206 <option value="Trematode_Mitochondrial">Trematode_Mitochondrial</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	207 <option value="Scenedesmus_obliquus_Mitochondrial">Scenedesmus_obliquus_Mitochondrial</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	208 <option value="Thraustochytrium_Mitochondrial">Thraustochytrium_Mitochondrial</option>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	209 </param>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	210 </when>
0 39bac90c773d Uploaded iuc parents: diff changeset	211 </conditional>
39bac90c773d Uploaded iuc parents: diff changeset	212
21 9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	213 <param name="udLength" argument="-ud" type="select" label="Upstream / Downstream length">
0 39bac90c773d Uploaded iuc parents: diff changeset	214 <option value="0">No upstream / downstream intervals (0 bases)</option>
39bac90c773d Uploaded iuc parents: diff changeset	215 <option value="200">200 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	216 <option value="500">500 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	217 <option value="1000">1000 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	218 <option value="2000">2000 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	219 <option value="5000" selected="true">5000 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	220 <option value="10000">10000 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	221 <option value="20000">20000 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	222 </param>
39bac90c773d Uploaded iuc parents: diff changeset	223
21 9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	224 <param name="spliceSiteSize" argument="-ss" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases">
0 39bac90c773d Uploaded iuc parents: diff changeset	225 <option value="1">1 base</option>
39bac90c773d Uploaded iuc parents: diff changeset	226 <option value="2" selected="true">2 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	227 <option value="3">3 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	228 <option value="4">4 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	229 <option value="5">5 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	230 <option value="6">6 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	231 <option value="7">7 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	232 <option value="8">8 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	233 <option value="9">9 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	234 </param>
39bac90c773d Uploaded iuc parents: diff changeset	235
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	236 <conditional name="spliceRegion">
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	237 <param name="setSpliceRegions" type="select" label="spliceRegion Settings">
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	238 <option value="no">Use Defaults</option>
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	239 <option value="yes">Set Splice Region Parameters</option>
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	240 </param>
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	241 <when value="no"/>
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	242 <when value="yes">
21 9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	243 <param argument="-spliceRegionExonSize" type="integer" value="" min="1" max="10" optional="true" label="Set size for splice site region within exons. Default: 3 bases" />
9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	244 <param argument="-spliceRegionIntronMin" type="integer" value="" min="1" max="10" optional="true" label="Set minimum number of bases for splice site region within intron. Default: 3 bases" />
9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	245 <param argument="-spliceRegionIntronMax" type="integer" value="" min="1" max="10" optional="true" label="Set maximum number of bases for splice site region within intron. Default: 8 bases" />
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	246 </when>
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	247 </conditional>
0 39bac90c773d Uploaded iuc parents: diff changeset	248
39bac90c773d Uploaded iuc parents: diff changeset	249 <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options">
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	250 <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN')</option>
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	251 <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>
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	252 <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option>
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	253 <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option>
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	254 <option value="-hgvsOld">Old notation style notation: E.g. 'c.G123T' instead of 'c.123G>T' and 'X' instead of '*'</option>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	255 <option value="-hgvs1LetterAa">Use one letter Amino acid codes in HGVS notation. E.g. p.R47G instead of p.Arg47Gly</option>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	256 <option value="-hgvsTrId">Use transcript ID in HGVS notation. E.g. ENST00000252100:c.914C>G instead of c.914C>G</option>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	257 <option value="-noShiftHgvs">Do not shift variants according to HGVS notation (most 3prime end)</option>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	258 <option value="-noHgvs">Do not add HGVS annotations</option>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	259 <option value="-canon">Only use canonical transcripts</option>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	260 <option value="-onlyProtein">Only use protein coding transcripts</option>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	261 <option value="-geneId">Use gene ID instead of gene name (VCF output)</option>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	262 <option value="-noExpandIUB">Disable IUB code expansion in input variants</option>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	263 <option value="-oicr">Add OICR tag in VCF file</option>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	264 <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	265 <option value="-noLof">Do not add LOF and NMD annotations</option>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	266 <option value="-noMotif">Disable motif annotations</option>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	267 <option value="-noNextProt">Disable NextProt annotations</option>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	268 <option value="-noInteraction">Disable interaction annotations</option>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	269 <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option>
12 bbbab2d84e3b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 9d2052269bfbca81a5f9cd10c3153e611358a329 iuc parents: 11 diff changeset	270 <!-- onlyReg option results in frequent exceptions with version 4.3k
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	271 <option value="-onlyReg">Only use regulation tracks</option>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	272 -->
0 39bac90c773d Uploaded iuc parents: diff changeset	273 </param>
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	274 <!-- -cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples. -->
21 9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	275 <param name="intervals" argument="-interval" type="data" format="bed" optional="true" label="Use custom interval file for annotation" />
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	276 <param name="transcripts" type="data" format="tabular" optional="true" label="Only use the transcripts in this file" help="Format is one transcript ID per line"/>
0 39bac90c773d Uploaded iuc parents: diff changeset	277 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
39bac90c773d Uploaded iuc parents: diff changeset	278 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
39bac90c773d Uploaded iuc parents: diff changeset	279 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
39bac90c773d Uploaded iuc parents: diff changeset	280 <option value="-no-intron">Do not show INTRON changes</option>
39bac90c773d Uploaded iuc parents: diff changeset	281 <option value="-no-upstream">Do not show UPSTREAM changes</option>
39bac90c773d Uploaded iuc parents: diff changeset	282 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option>
39bac90c773d Uploaded iuc parents: diff changeset	283 </param>
6 9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	284 <conditional name="filter">
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	285 <param name="specificEffects" type="select" label="Filter out specific Effects">
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	286 <option value="no">No</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	287 <option value="yes">Yes</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	288 </param>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	289 <when value="no"/>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	290 <when value="yes">
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	291 <param name="effects" type="select" display="checkboxes" multiple="true" label="Filter output: do not report these Effects">
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	292 <option value="CDS">CDS (coding_sequence_variant) The variant hits a CDS. MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	293 <option value="CHROMOSOME_LARGE_DELETION">CHROMOSOME_LARGE_DELETION (chromosome) A large parte (over 1%) of the chromosome was deleted. HIGH</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	294 <option value="CODON_CHANGE">CODON_CHANGE (coding_sequence_variant) One or many codons are changed e.g.: An MNP of size multiple of 3 MODERATE</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	295 <option value="CODON_INSERTION">CODON_INSERTION (inframe_insertion) One or many codons are inserted e.g.: An insert multiple of three in a codon boundary MODERATE</option>
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	296 <option value="CODON_CHANGE_PLUS_CODON_INSERTION">CODON_CHANGE_PLUS_CODON_INSERTION (disruptive_inframe_insertion) One codon is changed and one or many codons are inserted e.g.: An insert of size multiple of three, not at codon boundary MODERATE</option>
6 9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	297 <option value="CODON_DELETION">CODON_DELETION (inframe_deletion) One or many codons are deleted e.g.: A deletion multiple of three at codon boundary MODERATE</option>
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	298 <option value="CODON_CHANGE_PLUS_CODON_DELETION">CODON_CHANGE_PLUS_CODON_DELETION (disruptive_inframe_deletion) One codon is changed and one or more codons are deleted e.g.: A deletion of size multiple of three, not at codon boundary MODERATE</option>
6 9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	299 <option value="DOWNSTREAM">DOWNSTREAM (downstream_gene_variant) Downstream of a gene (default length: 5K bases) MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	300 <option value="EXON">EXON (exon_variant) The variant hits an exon (from a non-coding transcript) or a retained intron. MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	301 <option value="EXON_DELETED">EXON_DELETED (exon_loss_variant) A deletion removes the whole exon. HIGH</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	302 <option value="FRAME_SHIFT">FRAME_SHIFT (frameshift_variant) Insertion or deletion causes a frame shift e.g.: An indel size is not multple of 3 HIGH</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	303 <option value="GENE">GENE (gene_variant) The variant hits a gene. MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	304 <option value="INTERGENIC">INTERGENIC (intergenic_region) The variant is in an intergenic region MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	305 <option value="INTERGENIC_CONSERVED">INTERGENIC_CONSERVED (conserved_intergenic_variant) The variant is in a highly conserved intergenic region MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	306 <option value="INTRAGENIC">INTRAGENIC (intragenic_variant) The variant hits a gene, but no transcripts within the gene MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	307 <option value="INTRON">INTRON (intron_variant) Variant hits and intron. Technically, hits no exon in the transcript. MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	308 <option value="INTRON_CONSERVED">INTRON_CONSERVED (conserved_intron_variant) The variant is in a highly conserved intronic region MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	309 <option value="MICRO_RNA">MICRO_RNA (miRNA) Variant affects an miRNA MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	310 <option value="NON_SYNONYMOUS_CODING">NON_SYNONYMOUS_CODING (missense_variant) Variant causes a codon that produces a different amino acid e.g.: Tgg/Cgg, W/R MODERATE</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	311 <option value="NON_SYNONYMOUS_START">NON_SYNONYMOUS_START (initiator_codon_variant) Variant causes start codon to be mutated into another start codon (the new codon produces a different AA). e.g.: Atg/Ctg, M/L (ATG and CTG can be START codons) LOW</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	312 <option value="NON_SYNONYMOUS_STOP">NON_SYNONYMOUS_STOP (stop_retained_variant) Variant causes stop codon to be mutated into another stop codon (the new codon produces a different AA). e.g.: Atg/Ctg, M/L (ATG and CTG can be START codons) LOW</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	313 <option value="RARE_AMINO_ACID">RARE_AMINO_ACID (rare_amino_acid_variant) The variant hits a rare amino acid thus is likely to produce protein loss of function HIGH</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	314 <option value="SPLICE_SITE_ACCEPTOR">SPLICE_SITE_ACCEPTOR (splice_acceptor_variant) The variant hits a splice acceptor site (defined as two bases before exon start, except for the first exon). HIGH</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	315 <option value="SPLICE_SITE_DONOR">SPLICE_SITE_DONOR (splice_donor_variant) The variant hits a Splice donor site (defined as two bases after coding exon end, except for the last exon). HIGH</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	316 <option value="SPLICE_SITE_REGION">SPLICE_SITE_REGION (splice_region_variant) A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. LOW</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	317 <option value="SPLICE_SITE_BRANCH">SPLICE_SITE_BRANCH (splice_region_variant) A varaint affective putative (Lariat) branch point, located in the intron. LOW</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	318 <option value="SPLICE_SITE_BRANCH_U12">SPLICE_SITE_BRANCH_U12 (splice_region_variant) A varaint affective putative (Lariat) branch point from U12 splicing machinery, located in the intron. MODERATE</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	319 <option value="STOP_LOST">STOP_LOST (stop_lost) Variant causes stop codon to be mutated into a non-stop codon e.g.: Tga/Cga, */R HIGH</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	320 <option value="START_GAINED">START_GAINED (5_prime_UTR_premature start_codon_gain_variant) A variant in 5'UTR region produces a three base sequence that can be a START codon. LOW</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	321 <option value="START_LOST">START_LOST (start_lost) Variant causes start codon to be mutated into a non-start codon. e.g.: aTg/aGg, M/R HIGH</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	322 <option value="STOP_GAINED">STOP_GAINED (stop_gained) Variant causes a STOP codon e.g.: Cag/Tag, Q/* HIGH</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	323 <option value="SYNONYMOUS_CODING">SYNONYMOUS_CODING (synonymous_variant) Variant causes a codon that produces the same amino acid e.g.: Ttg/Ctg, L/L LOW</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	324 <option value="SYNONYMOUS_START">SYNONYMOUS_START (start_retained) Variant causes start codon to be mutated into another start codon. e.g.: Ttg/Ctg, L/L (TTG and CTG can be START codons) LOW</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	325 <option value="SYNONYMOUS_STOP">SYNONYMOUS_STOP (stop_retained_variant) Variant causes stop codon to be mutated into another stop codon. e.g.: taA/taG, / LOW</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	326 <option value="TRANSCRIPT">TRANSCRIPT (transcript_variant) The variant hits a transcript. MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	327 <option value="REGULATION">REGULATION (regulatory_region_variant) The variant hits a known regulatory feature (non-coding). MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	328 <option value="UPSTREAM">UPSTREAM (upstream_gene_variant) Upstream of a gene (default length: 5K bases) MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	329 <option value="UTR_3_PRIME">UTR_3_PRIME (3_prime_UTR_variant) Variant hits 3'UTR region MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	330 <option value="UTR_3_DELETED">UTR_3_DELETED (3_prime_UTR_truncation + exon_loss) The variant deletes an exon which is in the 3'UTR of the transcript MODERATE</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	331 <option value="UTR_5_PRIME">UTR_5_PRIME (5_prime_UTR_variant) Variant hits 5'UTR region MODIFIER</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	332 <option value="UTR_5_DELETED">UTR_5_DELETED (5_prime_UTR_truncation + exon_loss_variant) The variant deletes an exon which is in the 5'UTR of the transcript MODERATE</option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	333 <option value="NEXT_PROT">NEXT_PROT (sequence_feature + exon_loss_variant) A 'NextProt' based annotation. Details are provided in the 'feature type' sub-field (ANN), or in the effect details (EFF). MODERATE </option>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	334 </param>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	335 </when>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	336 </conditional>
0 39bac90c773d Uploaded iuc parents: diff changeset	337
21 9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	338 <param name="offset" type="select" display="radio" label="Chromosomal position">
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	339 <option value="default" selected="true">Use default (based on input type)</option>
0 39bac90c773d Uploaded iuc parents: diff changeset	340 <option value="-0">Force zero-based positions (both input and output)</option>
39bac90c773d Uploaded iuc parents: diff changeset	341 <option value="-1">Force one-based positions (both input and output)</option>
39bac90c773d Uploaded iuc parents: diff changeset	342 </param>
21 9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	343 <param argument="-chr" type="text" label="Text to prepend to chromosome name">
0 39bac90c773d Uploaded iuc parents: diff changeset	344 <help>
39bac90c773d Uploaded iuc parents: diff changeset	345 By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'.
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	346 You can prepend any string you want to the chromosome name
0 39bac90c773d Uploaded iuc parents: diff changeset	347 </help>
39bac90c773d Uploaded iuc parents: diff changeset	348 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
39bac90c773d Uploaded iuc parents: diff changeset	349 </param>
21 9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	350 <param name="generate_stats" argument="-noStats" type="boolean" truevalue="" falsevalue="-noStats" checked="true" label="Produce Summary Stats" />
9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	351 <param argument="-noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server" />
0 39bac90c773d Uploaded iuc parents: diff changeset	352 </inputs>
39bac90c773d Uploaded iuc parents: diff changeset	353 <outputs>
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	354 <data name="snpeff_output" format="vcf">
0 39bac90c773d Uploaded iuc parents: diff changeset	355 <change_format>
39bac90c773d Uploaded iuc parents: diff changeset	356 <when input="outputConditional.outputFormat" value="bed" format="bed" />
39bac90c773d Uploaded iuc parents: diff changeset	357 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
39bac90c773d Uploaded iuc parents: diff changeset	358 </change_format>
39bac90c773d Uploaded iuc parents: diff changeset	359 </data>
18 a9b0163b9fab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 16 diff changeset	360 <data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats">
30 0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	361 <filter>generate_stats</filter>
0 39bac90c773d Uploaded iuc parents: diff changeset	362 </data>
18 a9b0163b9fab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 16 diff changeset	363 <data name="csvFile" format="csv" label="${tool.name} on ${on_string} - CSV stats">
30 0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	364 <filter>csvStats</filter>
18 a9b0163b9fab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 31abf30ef7abe008e23cb9eadd5268649a00035b iuc parents: 16 diff changeset	365 </data>
0 39bac90c773d Uploaded iuc parents: diff changeset	366 </outputs>
39bac90c773d Uploaded iuc parents: diff changeset	367 <tests>
30 0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	368 <test expect_num_outputs="2">
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	369 <param name="input" ftype="vcf" value="input.vcf"/>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	370 <param name="inputFormat" value="vcf"/>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	371 <param name="outputFormat" value="vcf"/>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	372 <param name="genomeSrc" value="named"/>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	373 <param name="genome_version" value="ebola_zaire"/>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	374 <param name="udLength" value="0"/>
30 0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	375 <param name="generate_stats" value="true"/>
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	376 <output name="snpeff_output">
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	377 <assert_contents>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	378 <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	379 <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	380 </assert_contents>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	381 </output>
30 0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	382 <output name="statsFile">
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	383 <assert_contents>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	384 <has_text text="<b>"/>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	385 </assert_contents>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	386 </output>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	387 </test>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	388 <!-- Test interval option-->
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	389 <test expect_num_outputs="2">
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	390 <param name="input" ftype="vcf" value="input.vcf"/>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	391 <param name="inputFormat" value="vcf"/>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	392 <param name="outputFormat" value="vcf"/>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	393 <param name="genomeSrc" value="named"/>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	394 <param name="interval" value="intervals.bed"/>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	395 <param name="genome_version" value="ebola_zaire"/>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	396 <param name="udLength" value="0"/>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	397 <param name="generate_stats" value="false"/>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	398 <param name="csvStats" value="true"/>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	399 <output name="snpeff_output">
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	400 <assert_contents>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	401 <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	402 <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	403 </assert_contents>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	404 </output>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	405 <output name="csvFile">
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	406 <assert_contents>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	407 <has_n_lines n="185"/>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	408 <has_n_columns n="1" sep=","/>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	409 </assert_contents>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	410 </output>
0 39bac90c773d Uploaded iuc parents: diff changeset	411 </test>
39bac90c773d Uploaded iuc parents: diff changeset	412 </tests>
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	413 <help><![CDATA[
14 a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	414 What it does
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	415
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	416 SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	417
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	418 A typical SnpEff use case would be:
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	419
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	420 - Input: The inputs are predicted variants (SNPs, insertions, deletions and MNPs). The input file is usually obtained as a result of a sequencing experiment, and it is usually in variant call format (VCF).
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	421 - Output: SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes). A list of effects and annotations that SnpEff can calculate can be found here.
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	422
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	423 By genetic variant we mean difference between a genome and a "reference" genome. As an example, imagine we are sequencing a "sample". Here "sample" can mean anything that you are interested in studying, from a cell culture, to a mouse or a cancer patient. It is a standard procedure to compare your sample sequences against the corresponding "reference genome". For instance you may compare the cancer patient genome against the "reference genome".
0 39bac90c773d Uploaded iuc parents: diff changeset	424
16 7c4ede6d88a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71 iuc parents: 14 diff changeset	425 In a typical sequencing experiment, you will find many places in the genome where your sample differs from the reference genome. These are called "genomic variants" or just "variants".
14 a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	426 Typically, variants are categorized as follows:
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	427
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	428 - SNP (Single-Nucleotide Polymorphism) Reference = 'A', Sample = 'C'
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	429 - Ins (Insertion) Reference = 'A', Sample = 'AGT'
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	430 - Del (Deletion) Reference = 'AC', Sample = 'C'
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	431 - MNP (Multiple-nucleotide polymorphism) Reference = 'ATA', Sample = 'GTC'
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	432 - MIXED (Multiple-nucleotide and an InDel) Reference = 'ATA', Sample = 'GTCAGT'
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	433
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	434 This is not a comprehensive list, it is just to give you an idea.
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	435
16 7c4ede6d88a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71 iuc parents: 14 diff changeset	436 Suppose you have a huge file describing all the differences between your sample and the reference genome. But you want to know more about these variants than just their genetic coordinates. E.g.: Are they in a gene? In an exon? Do they change protein coding? Do they cause premature stop codons? SnpEff can help you answer all these questions. The process of adding this information about the variants is called "Annotation".
14 a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	437 SnpEff provides several degrees of annotations, from simple (e.g. which gene is each variant affecting) to extremely complex annotations (e.g. will this non-coding variant affect the expression of a gene?). It should be noted that the more complex the annotations, the more it relies in computational predictions. Such computational predictions can be incorrect, so results from SnpEff (or any prediction algorithm) cannot be trusted blindly, they must be analyzed and independently validated by corresponding wet-lab experiments.
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	438
21 9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	439 @SNPEFF_IN_GALAXY_INFO@
9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	440 @EXTERNAL_DOCUMENTATION@
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	441 ]]>
0 39bac90c773d Uploaded iuc parents: diff changeset	442 </help>
39bac90c773d Uploaded iuc parents: diff changeset	443 <expand macro="citations" />
39bac90c773d Uploaded iuc parents: diff changeset	444 </tool>

Mercurial > repos > iuc > snpeff

annotate snpEff.xml @ 30:0c8a8cd9dd5b draft