Mercurial > repos > iuc > gemini_pathways

annotate gemini_pathways.xml @ 2:71c51883304f draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
author iuc
date Tue, 16 Feb 2016 05:55:52 -0500
parents 668b63ef3402
children 1e10a153192d
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668b63ef3402 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
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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 <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[
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12 gemini
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13 #if $annotation_databases:
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14 --annotation-dir "${annotation_databases.fields.path}"
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15 #end if
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16 @BINARY@
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17 -v $ensembl
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18 $lof
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19 "${ infile }"
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20 > "${ outfile }"
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21 ]]>
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22 </command>
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23 <inputs>
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24 <expand macro="infile" />
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25
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26 <param name="ensembl" type="integer" value="68" label="Version of ensembl genes to use"
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27 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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28 <validator type="in_range" min="66" max="71"/>
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29 </param>
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30
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31 <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False"
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32 label="Report only pathways with loss-of-function variants" help="(--lof)"/>
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33 <expand macro="annotation_dir" />
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34 </inputs>
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35 <outputs>
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36 <data name="outfile" format="tabular" />
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" />
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41 <param name="ensembl" value="68" />
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42 <output name="outfile" file="gemini_pathways_result.tabular" />
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43 </test>
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44 </tests>
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45 <help>
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46 **What it does**
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47
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48 Mapping genes to biological pathways is useful in understanding the function/role played by a gene.
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49 Likewise, genes involved in common pathways is helpful in understanding heterogeneous diseases.
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50 We have integrated the KEGG pathway mapping for gene variants, to explain/annotate variation.
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51
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52 This requires your VCF be annotated with either snpEff/VEP.
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53
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54 </help>
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55 <expand macro="citations"/>
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56 </tool>