Mercurial > repos > iuc > snpsift_genesets

comparison snpSift_geneSets.xml @ 3:847db7b39bdc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:06:09 -0500
parents 9ba6e2c298ab
children d12a810c837e
comparison
equal deleted inserted replaced
2:9ba6e2c298ab 3:847db7b39bdc
1 <tool id="snpSift_geneSets" name="SnpSift GeneSets" version="@WRAPPER_VERSION@.0"> 1 <tool id="snpSift_geneSets" name="SnpSift GeneSets" version="@WRAPPER_VERSION@.1">
2 <description>Annotating GeneSets, such as Gene Ontology, KEGG, Reactome</description> 2 <description>Annotating GeneSets, such as Gene Ontology, KEGG, Reactome</description>
3 <!-- 3 <!--
4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) 4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
5 --> 5 -->
6 <macros> 6 <macros>
8 </macros> 8 </macros>
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <expand macro="version_command" /> 11 <expand macro="version_command" />
12 <command><![CDATA[ 12 <command><![CDATA[
13 @CONDA_SNPEFF_JAR_PATH@ && 13 @CONDA_SNPSIFT_JAR_PATH@ &&
14 java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" geneSets -v 14 java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" geneSets -v
15 #if $db_opts.db_opts_selector == "db" 15 #if $db_opts.db_opts_selector == "db"
16 "${db_opts.database.fields.path}" 16 "${db_opts.database.fields.path}"
17 #elif $db_opts.db_opts_selector == "histdb" 17 #elif $db_opts.db_opts_selector == "histdb"
18 "$db_opts.histdb" 18 "$db_opts.histdb"
19 #end if 19 #end if
53 53
54 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. 54 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.
55 55
56 @EXTERNAL_DOCUMENTATION@ 56 @EXTERNAL_DOCUMENTATION@
57 57
58 @CITATION_SECTION@
59
60 For `MSigDB`_, please cite |Subramanian2005|_.
61
62 .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/ 58 .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/
63 .. |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
64 .. _Subramanian2005: http://www.pnas.org/content/102/43/15545
65
66 ]]> 59 ]]>
67 </help> 60 </help>
68 <expand macro="citations"> 61 <expand macro="citations">
69 <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation --> 62 <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation -->
70 </expand> 63 </expand>