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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
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2 <description>Map genes and variants to KEGG pathways</description>
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3 <expand macro="requirements" />
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4 <expand macro="version_command" />
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5 <macros>
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6 <import>gemini_macros.xml</import>
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7 <token name="@BINARY@">pathways</token>
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8 </macros>
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9 <command>
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10 <![CDATA[
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11 gemini
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12 --annotation-dir ${annotation_databases.fields.path}
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13 @BINARY@
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14 -v $ensembl
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15 $lof
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16 "${ infile }"
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17 > "${ outfile }"
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18 ]]>
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19 </command>
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20 <expand macro="stdio" />
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21 <inputs>
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22 <param name="infile" type="data" format="sqlite" label="GEMINI database" />
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23
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24 <param name="ensembl" type="integer" value="68" size="5" label="Version of ensembl genes to use"
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25 help="Supported versions: 66 to 71. use versions that match the VEP/snpEff versions of the annotated vcf for correctness. For e.g VEP v2.6 and snpEff v3.1 use Ensembl 68 version of the genomes. (-v)">
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26 <validator type="in_range" min="66" max="71"/>
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27 </param>
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28
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29 <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False"
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30 label="Report only pathways with loss-of-function variants" help="(--lof)"/>
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31 <expand macro="annotation_dir" />
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32 </inputs>
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33 <outputs>
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34 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
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35 </outputs>
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36 <tests>
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37 <test>
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38 </test>
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39 </tests>
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40 <help>
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41 **What it does**
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42
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43 Mapping genes to biological pathways is useful in understanding the function/role played by a gene.
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44 Likewise, genes involved in common pathways is helpful in understanding heterogeneous diseases.
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45 We have integrated the KEGG pathway mapping for gene variants, to explain/annotate variation.
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46
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47 This requires your VCF be annotated with either snpEff/VEP.
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48
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49 @CITATION@
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50 </help>
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51 <expand macro="citations"/>
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52 </tool>
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