Mercurial > repos > iuc > snpsift_genesets

annotate snpSift_geneSets.xml @ 4:71daf733a39e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit fbc18d9128669e461e76ed13307ee88dd774afa5
author iuc
date Mon, 12 Jun 2017 10:25:06 -0400
parents 5a559dfb41a0
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71daf733a39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit fbc18d9128669e461e76ed13307ee88dd774afa5
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1 <tool id="snpSift_geneSets" name="SnpSift GeneSets" version="@WRAPPER_VERSION@.0">
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2 <description>Annotating GeneSets, such as Gene Ontology, KEGG, Reactome</description>
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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)
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5 -->
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6 <macros>
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7 <import>snpSift_macros.xml</import>
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8 </macros>
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9 <expand macro="requirements" />
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10 <expand macro="stdio" />
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11 <expand macro="version_command" />
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12 <command><![CDATA[
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13 SnpSift -Xmx2G geneSets -v
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14 #if $db_opts.db_opts_selector == 'db'
71daf733a39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit fbc18d9128669e461e76ed13307ee88dd774afa5
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15 '${db_opts.database.fields.path}'
71daf733a39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit fbc18d9128669e461e76ed13307ee88dd774afa5
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16 #elif $db_opts.db_opts_selector == 'histdb'
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17 '$db_opts.histdb'
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18 #end if
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19 '$input'
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20 2> '$log'
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21 > '$output'
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22 ]]></command>
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23 <inputs>
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24 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
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25 <conditional name="db_opts">
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26 <param name="db_opts_selector" type="select" label="Select Annotation database" help="">
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27 <option value="db" selected="True">Locally installed database</option>
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28 <option value="histdb">database from your history</option>
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29 </param>
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30 <when value="db">
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31 <param name="database" type="select" label="Molecular Signatures Database (MSigDB)">
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32 <options from_data_table="snpeff_msigdb_database" />
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33 </param>
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34 <param name="histdb" type="hidden" value="" />
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35 </when>
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36 <when value="histdb">
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37 <param name="histdb" type="data" format="txt" label="Molecular Signatures Database (MSigDB)" />
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38 </when>
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39 </conditional>
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40 </inputs>
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41 <outputs>
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42 <data name="output" format="vcf" label="${tool.name} on ${on_string}: VCF" />
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43 <data name="log" format="txt" label="${tool.name} on ${on_string}: log" />
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44 </outputs>
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45 <tests>
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46 </tests>
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47 <help><![CDATA[
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48 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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49
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50 .. _SnpSift GeneSets: http://snpeff.sourceforge.net/SnpSift.html#geneSets
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51
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52 .. class:: warningmark
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53
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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.
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55
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56 @EXTERNAL_DOCUMENTATION@
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57
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58 .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/
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59 ]]></help>
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60 <expand macro="citations">
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61 <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation -->
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62 </expand>
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63 </tool>