|
0
|
1 <tool id="snpSift_geneSets" name="SnpSift GeneSets" version="@WRAPPER_VERSION@.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 <macros>
|
|
|
7 <import>snpSift_macros.xml</import>
|
|
|
8 </macros>
|
|
|
9 <expand macro="requirements" />
|
|
|
10 <expand macro="stdio" />
|
|
|
11 <expand macro="version_command" />
|
|
|
12 <command><![CDATA[
|
|
|
13 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar geneSets -v
|
|
|
14 #if $db_opts.db_opts_selector == "db"
|
|
|
15 "${db_opts.database.fields.path}"
|
|
|
16 #elif $db_opts.db_opts_selector == "histdb"
|
|
|
17 "$db_opts.histdb"
|
|
|
18 #end if
|
|
|
19 $input 2> $log > $output
|
|
|
20 ]]>
|
|
|
21 </command>
|
|
|
22 <inputs>
|
|
|
23 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
|
|
|
24 <conditional name="db_opts">
|
|
|
25 <param name="db_opts_selector" type="select" label="Select Annotation database" help="">
|
|
|
26 <option value="db" selected="True">Locally installed database</option>
|
|
|
27 <option value="histdb">database from your history</option>
|
|
|
28 </param>
|
|
|
29 <when value="db">
|
|
|
30 <param name="database" type="select" label="Molecular Signatures Database (MSigDB)">
|
|
|
31 <options from_data_table="snpeff_msigdb_database" />
|
|
|
32 </param>
|
|
|
33 <param name="histdb" type="hidden" value="" />
|
|
|
34 </when>
|
|
|
35 <when value="histdb">
|
|
|
36 <param name="histdb" type="data" format="txt" label="Molecular Signatures Database (MSigDB)" />
|
|
|
37 </when>
|
|
|
38 </conditional>
|
|
|
39 </inputs>
|
|
|
40 <outputs>
|
|
|
41 <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" />
|
|
|
42 <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
|
|
|
43 </outputs>
|
|
|
44 <tests>
|
|
|
45 </tests>
|
|
|
46 <help><![CDATA[
|
|
|
47 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.
|
|
|
48
|
|
|
49 .. _SnpSift GeneSets: http://snpeff.sourceforge.net/SnpSift.html#geneSets
|
|
|
50
|
|
|
51 .. class:: warningmark
|
|
|
52
|
|
|
53 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
|
|
|
55 @EXTERNAL_DOCUMENTATION@
|
|
|
56
|
|
|
57 @CITATION_SECTION@
|
|
|
58
|
|
|
59 For `MSigDB`_, please cite |Subramanian2005|_.
|
|
|
60
|
|
|
61 .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/
|
|
|
62 .. |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
|
|
|
63 .. _Subramanian2005: http://www.pnas.org/content/102/43/15545
|
|
|
64
|
|
|
65 ]]>
|
|
|
66 </help>
|
|
|
67 <expand macro="citations">
|
|
|
68 <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation -->
|
|
|
69 </expand>
|
|
|
70 </tool>
|
