Mercurial > repos > jjohnson > snpeff
changeset 12:6d429d880a75
Update for snpeff version 4.0
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Mon, 20 Oct 2014 08:37:01 -0500 |
parents | c5288d5a446e |
children | 4be8e0068bc3 |
files | lib/galaxy/datatypes/snpeff.pyc readme.rst snpEff.xml snpEff_download.xml snpEff_macros.xml tool_dependencies.xml |
diffstat | 6 files changed, 13 insertions(+), 8 deletions(-) [+] |
line wrap: on
line diff
--- a/readme.rst Thu Jun 26 08:40:30 2014 -0500 +++ b/readme.rst Mon Oct 20 08:37:01 2014 -0500 @@ -9,6 +9,10 @@ "SnpEff Download" snpEff_download.xml are taken from: tool-data/snpeffect_genomedb.loc +There are 2 datamanagers to download and install prebuilt SnpEff Genome databases: + data_manager_snpeff_databases - generates a list of available SnpEff genome databases into the tool-data/snpeff_databases.loc + data_manager_snpeff_download - downloads a SnpEff genome database selected from: tool-data/snpeff_databases.loc and adds entries to snpeff_genomedb.loc,snpeff_regulationdb.loc,snpeff_annotations.loc + SnpEff citation: "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
--- a/snpEff.xml Thu Jun 26 08:40:30 2014 -0500 +++ b/snpEff.xml Mon Oct 20 08:37:01 2014 -0500 @@ -1,4 +1,4 @@ -<tool id="snpEff" name="SnpEff" version="3.6"> +<tool id="snpEff" name="SnpEff" version="4.0.0"> <description>Variant effect and annotation</description> <expand macro="requirements" /> <macros> @@ -40,7 +40,7 @@ #if $chr.__str__.strip() != '': -chr "$chr" #end if - $noLog + $noLog #if $snpDb.genomeSrc == 'cached': -dataDir ${snpDb.genomeVersion.fields.path} #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': @@ -176,11 +176,12 @@ <option value="-cancer">Perform 'cancer' comparissons (Somatic vs Germline)</option> <option value="-canon">Only use canonical transcripts</option> <option value="-geneId">Use gene ID instead of gene name (VCF output)</option> - <option value="-hgvs">Use HGVS annotations for amino acid sub-field</option> <option value="-lof">Add loss of function (LOF) and Nonsense mediated decay (NMD) tags</option> <option value="-oicr">Add OICR tag in VCF file</option> <option value="-onlyReg">Only use regulation tracks</option> - <option value="-sequenceOntolgy">Use Sequence Ontolgy terms.</option> + <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> + <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option> + <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option> </param> <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/> <param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file." help="Format is one transcript ID per line."/>
--- a/snpEff_download.xml Thu Jun 26 08:40:30 2014 -0500 +++ b/snpEff_download.xml Mon Oct 20 08:37:01 2014 -0500 @@ -1,4 +1,4 @@ -<tool id="snpEff_download" name="SnpEff Download" version="3.6"> +<tool id="snpEff_download" name="SnpEff Download" version="4.0.0"> <description>Download a new database</description> <expand macro="requirements" /> <macros>
--- a/snpEff_macros.xml Thu Jun 26 08:40:30 2014 -0500 +++ b/snpEff_macros.xml Mon Oct 20 08:37:01 2014 -0500 @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="3.6">snpEff</requirement> + <requirement type="package" version="4.0">snpEff</requirement> </requirements> </xml> <xml name="stdio">
--- a/tool_dependencies.xml Thu Jun 26 08:40:30 2014 -0500 +++ b/tool_dependencies.xml Mon Oct 20 08:37:01 2014 -0500 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> - <package name="snpEff" version="3.6"> - <repository name="package_snpeff_3_6" owner="jjohnson" changeset_revision="849895b37940" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + <package name="snpEff" version="4.0"> + <repository name="package_snpeff_4_0" owner="jjohnson" changeset_revision="4ac635fc1781" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </package> </tool_dependency>