Mercurial > repos > iuc > gemini_pathways

annotate gemini_pathways.xml @ 3:1e10a153192d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
author iuc
date Fri, 07 Dec 2018 12:38:41 -0500
parents 71c51883304f
children 1e736aee3c8c
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
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2 <description>Map genes and variants to KEGG pathways</description>
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3 <macros>
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4 <import>gemini_macros.xml</import>
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5 <token name="@BINARY@">pathways</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
3
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12 @PROVIDE_ANNO_DATA@
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13
0
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14 gemini
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15 @BINARY@
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16 -v $ensembl
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17 $lof
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18 "${ infile }"
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19 > "${ outfile }"
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20 ]]>
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21 </command>
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22 <inputs>
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23 <expand macro="infile" />
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25 <param name="ensembl" type="integer" value="68" label="Version of ensembl genes to use"
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26 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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27 <validator type="in_range" min="66" max="71"/>
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28 </param>
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29
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30 <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False"
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31 label="Report only pathways with loss-of-function variants" help="(--lof)"/>
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32 <expand macro="annotation_dir" />
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33 </inputs>
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34 <outputs>
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35 <data name="outfile" format="tabular" />
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" />
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40 <param name="ensembl" value="68" />
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41 <output name="outfile" file="gemini_pathways_result.tabular" />
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42 </test>
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43 </tests>
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44 <help>
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45 **What it does**
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46
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47 Mapping genes to biological pathways is useful in understanding the function/role played by a gene.
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48 Likewise, genes involved in common pathways is helpful in understanding heterogeneous diseases.
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49 We have integrated the KEGG pathway mapping for gene variants, to explain/annotate variation.
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50
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51 This requires your VCF be annotated with either snpEff/VEP.
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52
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53 </help>
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54 <expand macro="citations"/>
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55 </tool>