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comparison snpSift_geneSets.xml @ 1:0af41de4eda1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
author iuc
date Tue, 07 Jun 2016 10:05:20 -0400
parents 9e6fa49c1077
children 9ba6e2c298ab
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0:9e6fa49c1077 1:0af41de4eda1
1 <tool id="snpSift_geneSets" name="SnpSift GeneSets" version="4.0.0"> 1 <tool id="snpSift_geneSets" name="SnpSift GeneSets" version="@WRAPPER_VERSION@.0">
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 <expand macro="requirements" />
7 <macros> 6 <macros>
8 <import>snpSift_macros.xml</import> 7 <import>snpSift_macros.xml</import>
9 </macros> 8 </macros>
10 <command> 9 <expand macro="requirements" />
11 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar geneSets -v 10 <expand macro="stdio" />
11 <expand macro="version_command" />
12 <command><![CDATA[
13 java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" geneSets -v
12 #if $db_opts.db_opts_selector == "db" 14 #if $db_opts.db_opts_selector == "db"
13 "${db_opts.database.fields.path}" 15 "${db_opts.database.fields.path}"
14 #elif $db_opts.db_opts_selector == "histdb" 16 #elif $db_opts.db_opts_selector == "histdb"
15 "$db_opts.histdb" 17 "$db_opts.histdb"
16 #end if 18 #end if
17 19 "$input" 2> "$log" > "$output"
18 $input 2&gt; $log &gt; $output 20 ]]>
19 </command> 21 </command>
20 <inputs> 22 <inputs>
21 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> 23 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
22 <conditional name="db_opts"> 24 <conditional name="db_opts">
23 <param name="db_opts_selector" type="select" label="Select Annotation database" help=""> 25 <param name="db_opts_selector" type="select" label="Select Annotation database" help="">
37 </inputs> 39 </inputs>
38 <outputs> 40 <outputs>
39 <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" /> 41 <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" />
40 <data format="txt" name="log" label="${tool.name} on ${on_string}: log" /> 42 <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
41 </outputs> 43 </outputs>
42 <expand macro="stdio" />
43 <tests> 44 <tests>
44 </tests> 45 </tests>
45 <help> 46 <help><![CDATA[
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 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
48 .. _SnpSift GeneSets: http://snpeff.sourceforge.net/SnpSift.html#geneSets 49 .. _SnpSift GeneSets: http://snpeff.sourceforge.net/SnpSift.html#geneSets
49 50
50 .. class:: warningmark 51 .. class:: warningmark
58 For `MSigDB`_, please cite |Subramanian2005|_. 59 For `MSigDB`_, please cite |Subramanian2005|_.
59 60
60 .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/ 61 .. _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| 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 .. _Subramanian2005: http://www.pnas.org/content/102/43/15545
64
65 ]]>
63 </help> 66 </help>
64 <expand macro="citations"> 67 <expand macro="citations">
65 <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation --> 68 <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation -->
66 </expand> 69 </expand>
67 </tool> 70 </tool>