Mercurial > repos > iuc > snpsift_dbnsfp
changeset 93:ae7dfad9bba4 draft
Uploaded
author | iuc |
---|---|
date | Tue, 28 Apr 2015 22:37:13 -0400 |
parents | 426125d8923d |
children | ffaf4efb51fd |
files | snpSift_geneSets.xml tool-data/snpeff_msigdb_database.loc.sample |
diffstat | 2 files changed, 71 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpSift_geneSets.xml Tue Apr 28 22:37:13 2015 -0400 @@ -0,0 +1,67 @@ +<tool id="snpSift_geneSets" name="SnpSift GeneSets" version="4.0.0"> + <description>Annotating GeneSets, such as Gene Ontology, KEGG, Reactome</description> + <!-- + You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) + --> + <expand macro="requirements" /> + <macros> + <import>snpSift_macros.xml</import> + </macros> + <command> + java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar geneSets -v + #if $db_opts.db_opts_selector == "db" + "${db_opts.database.fields.path}" + #elif $db_opts.db_opts_selector == "histdb" + "$db_opts.histdb" + #end if + + $input 2> $log > $output + </command> + <inputs> + <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Select Annotation database" help=""> + <option value="db" selected="True">Locally installed database</option> + <option value="histdb">database from your history</option> + </param> + <when value="db"> + <param name="database" type="select" label="Molecular Signatures Database (MSigDB)"> + <options from_data_table="snpeff_msigdb_database" /> + </param> + <param name="histdb" type="hidden" value="" /> + </when> + <when value="histdb"> + <param name="histdb" type="data" format="txt" label="Molecular Signatures Database (MSigDB)" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" /> + <data format="txt" name="log" label="${tool.name} on ${on_string}: log" /> + </outputs> + <expand macro="stdio" /> + <tests> + </tests> + <help> +This tool uses `SnpSift GeneSets`_ to add annotations from `MSigDB`_, a collection of annotated gene sets from different sources including Gene Ontology (GO), KEGG, Reactome. + +.. _SnpSift GeneSets: http://snpeff.sourceforge.net/SnpSift.html#geneSets + +.. class:: warningmark + +The input VCF file must be annotated using SnpEff before performing GeneSets annotations. This is because the tool must know which gene the variant affects. + +@EXTERNAL_DOCUMENTATION@ + +@CITATION_SECTION@ + +For `MSigDB`_, please cite |Subramanian2005|_. + +.. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/ +.. |Subramanian2005| replace:: Subramanian, A., *et al.* (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. *Proc. Natl. Acad. Sci. U.S.A.* 102(43), 15545-15550 +.. _Subramanian2005: http://www.pnas.org/content/102/43/15545 + </help> + <expand macro="citations"> + <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation --> + </expand> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/snpeff_msigdb_database.loc.sample Tue Apr 28 22:37:13 2015 -0400 @@ -0,0 +1,4 @@ +## Molecular Signatures Database (MSigDB) for SnpEff. +## You can download MSigDb from http://www.broadinstitute.org/gsea/msigdb +#msigdb_id msigdb_name path_to_database +#msigdb_08_2014 MSigDB 08-2014 /data/msigdb/08_2014/msigdb.gmt