annotate snpSift_geneSets.xml @ 0:9e6fa49c1077 draft

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1 <tool id="snpSift_geneSets" name="SnpSift GeneSets" version="4.0.0">
2     <description>Annotating GeneSets, such as Gene Ontology, KEGG, Reactome</description>
3     <!-- 
4         You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
5     -->
6     <expand macro="requirements" />
7     <macros>
8         <import>snpSift_macros.xml</import>
9     </macros>
10     <command>
11         java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar geneSets -v
12         #if $db_opts.db_opts_selector == "db"
13           "${db_opts.database.fields.path}"
14         #elif $db_opts.db_opts_selector == "histdb"
15           "$db_opts.histdb"
16         #end if
17         
18         $input 2&gt; $log &gt; $output
19     </command>
20     <inputs>
21         <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
22         <conditional name="db_opts">
23             <param name="db_opts_selector" type="select" label="Select Annotation database" help="">
24               <option value="db" selected="True">Locally installed database</option>
25               <option value="histdb">database from your history</option>
26             </param>
27             <when value="db">
28                 <param name="database" type="select" label="Molecular Signatures Database (MSigDB)">
29                     <options from_data_table="snpeff_msigdb_database" />
30                 </param>
31                 <param name="histdb" type="hidden" value="" />
32             </when>
33             <when value="histdb">
34                 <param name="histdb" type="data" format="txt" label="Molecular Signatures Database (MSigDB)" />
35             </when>
36         </conditional>
37     </inputs>
38     <outputs>
39         <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" />
40         <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
41     </outputs>
42     <expand macro="stdio" />
43     <tests>
44     </tests>
45     <help>
46 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.
47 
48 .. _SnpSift GeneSets: http://snpeff.sourceforge.net/SnpSift.html#geneSets
49 
50 .. class:: warningmark
51 
52 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.
53 
54 @EXTERNAL_DOCUMENTATION@
55 
56 @CITATION_SECTION@
57 
58 For `MSigDB`_, please cite |Subramanian2005|_.
59 
60 .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/
61 .. |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
62 .. _Subramanian2005: http://www.pnas.org/content/102/43/15545
63     </help>
64     <expand macro="citations">
65         <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation -->
66     </expand>
67 </tool>