snpeff: snpEff.xml annotate

annotate snpEff.xml @ 33:94653948fdb9 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5

author	iuc
date	Sat, 04 Oct 2025 17:00:46 +0000
parents	ebe9fd7e5bd1
children

rev	line source
32 ebe9fd7e5bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 280d5247becaa9a70db9c5c4a2f1fc50d302838a iuc parents: 31 diff changeset	1 <tool id="snpEff" name="SnpEff eff:" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
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>
33 94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	7 <expand macro="requirement">
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	8 <requirement type="package" version="9.5">coreutils</requirement>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	9 </expand>
14 a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	10 </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	11 <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	12 <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	13 <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	14 #if $intervals
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	15 ln -s '${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	16 #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	17 snpEff @JAVA_OPTIONS@ eff
31 b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	18 -i $inputFormat -o ${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	19 #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	20 -spliceSiteSize "$spliceSiteSize"
0 39bac90c773d Uploaded iuc parents: diff changeset	21 #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	22 #if $spliceRegion.setSpliceRegions == 'yes':
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	23 #if str($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	24 -spliceRegionExonSize $spliceRegion.spliceRegionExonSize
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	25 #end if
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	26 #if str($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	27 -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	28 #end if
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	29 #if str($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	30 -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	31 #end if
0 39bac90c773d Uploaded iuc parents: diff changeset	32 #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	33 #if $annotations and str($annotations) != '':
0 39bac90c773d Uploaded iuc parents: diff changeset	34 #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	35 #echo ' '.join(str($annotations).split(','))
0 39bac90c773d Uploaded iuc parents: diff changeset	36 #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	37 #if $filterOut and str($filterOut) != '':
0 39bac90c773d Uploaded iuc parents: diff changeset	38 #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	39 #echo ' '.join(str($filterOut).split(','))
0 39bac90c773d Uploaded iuc parents: diff changeset	40 #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	41 #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	42 #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	43 -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	44 #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	45 #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	46 #if $transcripts
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	47 -onlyTr '$transcripts'
0 39bac90c773d Uploaded iuc parents: diff changeset	48 #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	49 #if $intervals ### fix this for multiple dataset input
30 0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	50 -interval intervals.bed
0 39bac90c773d Uploaded iuc parents: diff changeset	51 #end if
7 aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	52 #if str($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	53 -chr '$chr'
0 39bac90c773d Uploaded iuc parents: diff changeset	54 #end if
33 94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	55 #if $generate_stats or $generate_gene_stats or $csvStats:
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	56 #if $csvStats:
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	57 $csvStats snpeff_stats.csv
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	58 #end if
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	59 #if $generate_stats or ($generate_gene_stats and not $csvStats):
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	60 ## the base name passed in via the -csvStats or the -s option also determines the name of the genes.txt file
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	61 ## so in the absence of the first we need the second to have a consistent name of the genes.txt file
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	62 -s snpeff_stats.html
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	63 #end if
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	64 #else:
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	65 ## when no stats output is requested by the user, we can make things a little more efficient
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	66 ## by telling snpEff that it doesn't have to write even the default (html and genes.txt) ones.
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	67 -noStats
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	68 #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	69 $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	70 ## 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	71 ## 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	72 #if $snpDb.genomeSrc == 'cached':
39bac90c773d Uploaded iuc parents: diff changeset	73 -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	74 #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	75 #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	76 #for reg in $regs:
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	77 -reg '"${reg}"'
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	78 #end for
0 39bac90c773d Uploaded iuc parents: diff changeset	79 #end if
39bac90c773d Uploaded iuc parents: diff changeset	80 $snpDb.genomeVersion
39bac90c773d Uploaded iuc parents: diff changeset	81 #elif $snpDb.genomeSrc == 'history':
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	82 -dataDir '${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	83 #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	84 #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	85 #for reg in $regs:
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	86 -reg '"${reg}"'
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	87 #end for
0 39bac90c773d Uploaded iuc parents: diff changeset	88 #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	89 '${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	90 #elif $snpDb.genomeSrc == 'custom':
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	91 -dataDir '${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	92 -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	93 -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	94 '${snpDb.snpeff_db.metadata.genome_version}'
5 92b80578fa22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 2 diff changeset	95 #else
24 4c790901c495 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa iuc parents: 21 diff changeset	96 -dataDir "\$PWD/temp"
0 39bac90c773d Uploaded iuc parents: diff changeset	97 -download
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	98 '$snpDb.genome_version'
0 39bac90c773d Uploaded iuc parents: diff changeset	99 #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	100 '$input' > '$snpeff_output'
33 94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	101 #if $generate_gene_stats:
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	102 ## remove the first, unnecessary comment line from the output
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	103 && tail -n+2 snpeff_stats.genes.txt > genes.txt
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	104 #end if
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	105 #if $generate_stats:
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	106 ## independently of whether the user asked for the gene.txt file,
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	107 ## we need to add it to files_path because the stats html report links to it.
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	108 && mkdir '$statsFile.files_path' &&
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	109 mv snpeff_stats.genes.txt $statsFile.files_path
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)"/>
31 b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	114 <param argument="-i" name="inputFormat" type="select" label="Input format" help="Specify the format of input dataset(s)">
0 39bac90c773d Uploaded iuc parents: diff changeset	115 <option value="vcf" selected="true">VCF</option>
31 b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	116 <option value="bed">BED</option>
0 39bac90c773d Uploaded iuc parents: diff changeset	117 </param>
31 b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	118 <param argument="-o" name="outputFormat" type="select" label="Output format" help="Specify output format">
b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	119 <option value="vcf" selected="true">VCF (only if input is VCF)</option>
b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	120 <option value="gatk">GATK-compatible VCF (only if input is VCF)</option>
b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	121 <option value="bed">BED</option>
b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	122 <option value="bedAnn">BED annotations</option>
b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	123 </param>
b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	124 <param argument="-csvStats" type="boolean" truevalue="-csvStats" falsevalue="" checked="false" label="Create CSV report?" help="Useful for downstream analyses and report generation" />
33 94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	125 <param name="generate_stats" type="boolean" checked="true" label="Produce Summary Stats?" help="Generates an HTML summary of results"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	126 <param name="generate_gene_stats" type="boolean" label="Produce Gene Statistics output?" help="Generates a table of effects per gene as an extra output"/>
0 39bac90c773d Uploaded iuc parents: diff changeset	127 <conditional name="snpDb">
39bac90c773d Uploaded iuc parents: diff changeset	128 <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	129 <!-- 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	130 <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	131 <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	132 <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	133 <option value="custom">Custom snpEff database in your history</option>
0 39bac90c773d Uploaded iuc parents: diff changeset	134 </param>
39bac90c773d Uploaded iuc parents: diff changeset	135 <when value="cached">
39bac90c773d Uploaded iuc parents: diff changeset	136 <param name="genomeVersion" type="select" label="Genome">
39bac90c773d Uploaded iuc parents: diff changeset	137 <!--GENOME DESCRIPTION-->
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	138 <options from_data_table="snpeffv_genomedb">
33 94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	139 <filter type="regexp" column="1" value="@COMPATIBLE_DB_VERSIONS_REGEX@" />
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	140 <filter type="unique_value" column="2" />
0 39bac90c773d Uploaded iuc parents: diff changeset	141 </options>
39bac90c773d Uploaded iuc parents: diff changeset	142 </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	143 <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	144 <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	145 <options from_data_table="snpeffv_regulationdb">
33 94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	146 <filter type="regexp" column="1" value="@COMPATIBLE_DB_VERSIONS_REGEX@" />
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	147 <filter type="param_value" ref="genomeVersion" column="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	148 <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	149 </options>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	150 </param>
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>
0 39bac90c773d Uploaded iuc parents: diff changeset	152 </when>
39bac90c773d Uploaded iuc parents: diff changeset	153 <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	154 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
33 94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	155 <validator type="expression" message="This version of SnpEff will only work with @COMPATIBLE_DB_VERSIONS_STRING@ genome databases">value.metadata.snpeff_version in @COMPATIBLE_DB_VERSIONS@</validator>
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	156 </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	157 <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	158 <!-- 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	159 <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	160 <options>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	161 <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	162 </options>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	163 </param>
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>
0 39bac90c773d Uploaded iuc parents: diff changeset	165 </when>
39bac90c773d Uploaded iuc parents: diff changeset	166 <when value="named">
31 b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	167 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)" help="A list of databases can be obtained with 'snpEff download' tool">
21 9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	168 <validator type="empty_field" message="A genome version name is required" />
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	169 </param>
0 39bac90c773d Uploaded iuc parents: diff changeset	170 </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	171 <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	172 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
33 94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	173 <validator type="expression" message="This version of SnpEff will only work with @COMPATIBLE_DB_VERSIONS_STRING@ genome databases">value.metadata.snpeff_version in @COMPATIBLE_DB_VERSIONS@</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	174 </param>
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	175 <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	176 <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	177 <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	178 <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	179 <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	180 <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	181 <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	182 <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	183 <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	184 <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	185 <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	186 <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	187 <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	188 <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	189 <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	190 <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	191 <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	192 <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	193 <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	194 <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	195 <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	196 <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	197 <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	198 <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	199 <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	200 <option value="Thraustochytrium_Mitochondrial">Thraustochytrium_Mitochondrial</option>
33 94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	201 </param>
14 a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	202 </when>
0 39bac90c773d Uploaded iuc parents: diff changeset	203 </conditional>
21 9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	204 <param name="udLength" argument="-ud" type="select" label="Upstream / Downstream length">
31 b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	205 <option value="0" selected="true">No upstream / downstream intervals (0 bases)</option>
0 39bac90c773d Uploaded iuc parents: diff changeset	206 <option value="200">200 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	207 <option value="500">500 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	208 <option value="1000">1000 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	209 <option value="2000">2000 bases</option>
31 b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	210 <option value="5000">5000 bases</option>
0 39bac90c773d Uploaded iuc parents: diff changeset	211 <option value="10000">10000 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	212 <option value="20000">20000 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	213 </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	214 <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	215 <option value="1">1 base</option>
39bac90c773d Uploaded iuc parents: diff changeset	216 <option value="2" selected="true">2 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	217 <option value="3">3 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	218 <option value="4">4 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	219 <option value="5">5 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	220 <option value="6">6 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	221 <option value="7">7 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	222 <option value="8">8 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	223 <option value="9">9 bases</option>
39bac90c773d Uploaded iuc parents: diff changeset	224 </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	225 <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	226 <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	227 <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	228 <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	229 </param>
aaa749ea91a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 6 diff changeset	230 <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	231 <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	232 <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	233 <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	234 <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	235 </when>
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>
0 39bac90c773d Uploaded iuc parents: diff changeset	237 <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	238 <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN')</option>
2 114f423f99c0 Uploaded iuc parents: 0 diff changeset	239 <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	240 <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	241 <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	242 <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	243 <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	244 <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	245 <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	246 <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	247 <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	248 <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	249 <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	250 <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	251 <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	252 <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	253 <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	254 <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	255 <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	256 <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	257 <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	258 <!-- 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	259 <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	260 -->
0 39bac90c773d Uploaded iuc parents: diff changeset	261 </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	262 <!-- -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	263 <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	264 <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	265 <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output">
39bac90c773d Uploaded iuc parents: diff changeset	266 <option value="-no-downstream">Do not show DOWNSTREAM changes</option>
39bac90c773d Uploaded iuc parents: diff changeset	267 <option value="-no-intergenic">Do not show INTERGENIC changes</option>
39bac90c773d Uploaded iuc parents: diff changeset	268 <option value="-no-intron">Do not show INTRON changes</option>
39bac90c773d Uploaded iuc parents: diff changeset	269 <option value="-no-upstream">Do not show UPSTREAM changes</option>
39bac90c773d Uploaded iuc parents: diff changeset	270 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option>
39bac90c773d Uploaded iuc parents: diff changeset	271 </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	272 <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	273 <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	274 <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	275 <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	276 </param>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	277 <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	278 <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	279 <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	280 <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	281 <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	282 <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	283 <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	284 <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	285 <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	286 <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	287 <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	288 <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	289 <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	290 <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	291 <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	292 <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	293 <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	294 <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	295 <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	296 <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	297 <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	298 <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	299 <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	300 <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	301 <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	302 <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	303 <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	304 <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	305 <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	306 <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	307 <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	308 <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	309 <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	310 <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	311 <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	312 <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	313 <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	314 <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	315 <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	316 <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	317 <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	318 <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	319 <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	320 <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	321 <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	322 </param>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	323 </when>
9ec1cb6f760d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e5a5ad091c621348dc6ce2df861475ebc54a380e iuc parents: 5 diff changeset	324 </conditional>
21 9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	325 <param argument="-chr" type="text" label="Text to prepend to chromosome name">
0 39bac90c773d Uploaded iuc parents: diff changeset	326 <help>
39bac90c773d Uploaded iuc parents: diff changeset	327 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	328 You can prepend any string you want to the chromosome name
0 39bac90c773d Uploaded iuc parents: diff changeset	329 </help>
39bac90c773d Uploaded iuc parents: diff changeset	330 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
39bac90c773d Uploaded iuc parents: diff changeset	331 </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	332 <param argument="-noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server" />
0 39bac90c773d Uploaded iuc parents: diff changeset	333 </inputs>
39bac90c773d Uploaded iuc parents: diff changeset	334 <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	335 <data name="snpeff_output" format="vcf">
0 39bac90c773d Uploaded iuc parents: diff changeset	336 <change_format>
39bac90c773d Uploaded iuc parents: diff changeset	337 <when input="outputConditional.outputFormat" value="bed" format="bed" />
39bac90c773d Uploaded iuc parents: diff changeset	338 <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
39bac90c773d Uploaded iuc parents: diff changeset	339 </change_format>
39bac90c773d Uploaded iuc parents: diff changeset	340 </data>
33 94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	341 <data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats" from_work_dir="snpeff_stats.html">
30 0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	342 <filter>generate_stats</filter>
0 39bac90c773d Uploaded iuc parents: diff changeset	343 </data>
33 94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	344 <data name="genes_file" format="tabular" label="${tool.name} on ${on_string} - Gene stats" from_work_dir="genes.txt">
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	345 <filter>generate_gene_stats</filter>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	346 </data>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	347 <data name="csvFile" format="txt" label="${tool.name} on ${on_string} - CSV stats" from_work_dir="snpeff_stats.csv">
30 0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	348 <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	349 </data>
0 39bac90c773d Uploaded iuc parents: diff changeset	350 </outputs>
39bac90c773d Uploaded iuc parents: diff changeset	351 <tests>
33 94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	352 <test expect_num_outputs="1">
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	353 <param name="input" ftype="vcf" value="input.vcf"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	354 <param name="inputFormat" value="vcf"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	355 <param name="outputFormat" value="vcf"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	356 <conditional name="snpDb">
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	357 <param name="genomeSrc" value="cached"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	358 <param name="genomeVersion" value="ebola_zaire"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	359 </conditional>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	360 <param name="udLength" value="0"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	361 <param name="generate_stats" value="false"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	362 <output name="snpeff_output">
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	363 <assert_contents>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	364 <has_text_matching expression="KJ660346.1\t572\t.*missense_variant" />
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	365 <has_text_matching expression="KJ660346.1\t1024\t.*synonymous_variant" />
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	366 </assert_contents>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	367 </output>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	368 </test>
30 0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	369 <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	370 <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	371 <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	372 <param name="outputFormat" value="vcf"/>
33 94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	373 <conditional name="snpDb">
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	374 <param name="genomeSrc" value="cached"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	375 <param name="genomeVersion" value="ebola_zaire"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	376 </conditional>
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	377 <param name="udLength" value="0"/>
81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	378 <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	379 <assert_contents>
31 b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	380 <has_text_matching expression="KJ660346.1\t572\t.*missense_variant" />
b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	381 <has_text_matching expression="KJ660346.1\t1024\t.*synonymous_variant" />
11 81fba81425a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1 iuc parents: 9 diff changeset	382 </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	383 </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	384 <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	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 <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	387 </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	388 </output>
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>
33 94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	390 <test expect_num_outputs="2">
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	391 <param name="input" ftype="vcf" value="input.vcf"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	392 <param name="inputFormat" value="vcf"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	393 <param name="outputFormat" value="vcf"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	394 <conditional name="snpDb">
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	395 <param name="genomeSrc" value="cached"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	396 <param name="genomeVersion" value="ebola_zaire"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	397 </conditional>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	398 <param name="udLength" value="0"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	399 <param name="generate_stats" value="false"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	400 <param name="generate_gene_stats" value="true"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	401 <output name="snpeff_output">
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	402 <assert_contents>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	403 <has_text_matching expression="KJ660346.1\t572\t.*missense_variant" />
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	404 <has_text_matching expression="KJ660346.1\t1024\t.*synonymous_variant" />
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	405 </assert_contents>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	406 </output>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	407 <output name="genes_file">
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	408 <assert_contents>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	409 <has_text text="#GeneName"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	410 </assert_contents>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	411 </output>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	412 </test>
30 0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	413 <!-- 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	414 <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	415 <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	416 <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	417 <param name="outputFormat" value="vcf"/>
33 94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	418 <conditional name="snpDb">
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	419 <param name="genomeSrc" value="cached"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	420 <param name="genomeVersion" value="ebola_zaire"/>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	421 </conditional>
94653948fdb9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 iuc parents: 32 diff changeset	422 <param name="intervals" value="intervals.bed"/>
30 0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	423 <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	424 <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	425 <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	426 <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	427 <assert_contents>
31 b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	428 <has_text_matching expression="KJ660346.1\t572\t.*missense_variant" />
b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	429 <has_text_matching expression="KJ660346.1\t1024\t.*synonymous_variant" />
30 0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	430 </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	431 </output>
0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	432 <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	433 <assert_contents>
31 b7029a54f73e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7 iuc parents: 30 diff changeset	434 <has_n_lines n="134"/>
30 0c8a8cd9dd5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd iuc parents: 24 diff changeset	435 <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	436 </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	437 </output>
0 39bac90c773d Uploaded iuc parents: diff changeset	438 </test>
39bac90c773d Uploaded iuc parents: diff changeset	439 </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	440 <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	441 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	442
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	443 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	444
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	445 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	446
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	447 - 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	448 - 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	449
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	450 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	451
16 7c4ede6d88a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71 iuc parents: 14 diff changeset	452 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	453 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	454
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	455 - 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	456 - 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	457 - 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	458 - 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	459 - 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	460
a7c106b938dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef iuc parents: 13 diff changeset	461 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	462
16 7c4ede6d88a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71 iuc parents: 14 diff changeset	463 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	464 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	465
21 9939612ba3cf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102 iuc parents: 18 diff changeset	466 @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	467 @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	468 ]]>
0 39bac90c773d Uploaded iuc parents: diff changeset	469 </help>
39bac90c773d Uploaded iuc parents: diff changeset	470 <expand macro="citations" />
39bac90c773d Uploaded iuc parents: diff changeset	471 </tool>

Mercurial > repos > iuc > snpeff

annotate snpEff.xml @ 33:94653948fdb9 draft default tip