Mercurial > repos > iuc > snpsift_dbnsfp

annotate snpSift_geneSets.xml @ 199:ebf4eced9076 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 7b8a4ffc823f4dab194f1c629b7e83277dbe4337
author iuc
date Mon, 25 May 2015 22:37:20 -0400
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a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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1 <tool id="snpSift_geneSets" name="SnpSift GeneSets" version="4.0.0">
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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2 <description>Annotating GeneSets, such as Gene Ontology, KEGG, Reactome</description>
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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3 <!--
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4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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5 -->
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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6 <macros>
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7 <import>snpSift_macros.xml</import>
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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8 </macros>
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9 <expand macro="requirements" />
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10 <expand macro="stdio" />
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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11 <command>
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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12 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar geneSets -v
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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13 #if $db_opts.db_opts_selector == "db"
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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14 "${db_opts.database.fields.path}"
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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15 #elif $db_opts.db_opts_selector == "histdb"
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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16 "$db_opts.histdb"
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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17 #end if
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18
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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19 $input 2&gt; $log &gt; $output
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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20 </command>
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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21 <inputs>
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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22 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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23 <conditional name="db_opts">
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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24 <param name="db_opts_selector" type="select" label="Select Annotation database" help="">
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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25 <option value="db" selected="True">Locally installed database</option>
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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26 <option value="histdb">database from your history</option>
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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27 </param>
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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28 <when value="db">
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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29 <param name="database" type="select" label="Molecular Signatures Database (MSigDB)">
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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30 <options from_data_table="snpeff_msigdb_database" />
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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31 </param>
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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32 <param name="histdb" type="hidden" value="" />
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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33 </when>
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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34 <when value="histdb">
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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35 <param name="histdb" type="data" format="txt" label="Molecular Signatures Database (MSigDB)" />
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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36 </when>
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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37 </conditional>
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38 </inputs>
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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39 <outputs>
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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40 <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" />
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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41 <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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42 </outputs>
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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43 <tests>
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44 </tests>
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45 <help>
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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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.
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47
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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48 .. _SnpSift GeneSets: http://snpeff.sourceforge.net/SnpSift.html#geneSets
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49
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50 .. class:: warningmark
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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51
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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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.
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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54 @EXTERNAL_DOCUMENTATION@
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56 @CITATION_SECTION@
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a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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58 For `MSigDB`_, please cite |Subramanian2005|_.
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59
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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60 .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/
a7aed5f7a2ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets commit 344140b8df53b8b7024618bb04594607a045c03a
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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
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62 .. _Subramanian2005: http://www.pnas.org/content/102/43/15545
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63 </help>
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64 <expand macro="citations">
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65 <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation -->
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66 </expand>
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67 </tool>