Mercurial > repos > iuc > snpsift_dbnsfp
changeset 248:c0c68477e282 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit e5a5ad091c621348dc6ce2df861475ebc54a380e
| author | iuc |
|---|---|
| date | Tue, 13 Oct 2015 17:31:55 -0400 |
| parents | 818f4349ebd1 |
| children | 0775efb6a5f3 |
| files | snpSift_geneSets.xml tool-data/snpeff_msigdb_database.loc.sample |
| diffstat | 2 files changed, 0 insertions(+), 71 deletions(-) [+] |
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--- a/snpSift_geneSets.xml Sun Jun 28 22:51:05 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,67 +0,0 @@ -<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) - --> - <macros> - <import>snpSift_macros.xml</import> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <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> - <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>
--- a/tool-data/snpeff_msigdb_database.loc.sample Sun Jun 28 22:51:05 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -## 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