Mercurial > repos > iuc > gemini_pathways

annotate gemini_pathways.xml @ 5:1e736aee3c8c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author iuc
date Fri, 14 Dec 2018 12:37:34 -0500
parents 1e10a153192d
children 228263fd9c72
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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_load_result1.db" ftype="gemini.sqlite" />
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40 <param name="ensembl" value="68" />
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41 <output name="outfile">
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42 <assert_contents>
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43 <has_line_matching expression="chrom&#009;start&#009;end&#009;.*pathway.*" />
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44 </assert_contents>
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45 </output>
0
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46 </test>
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47 </tests>
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48 <help>
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49 **What it does**
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50
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51 Mapping genes to biological pathways is useful in understanding the function/role played by a gene.
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52 Likewise, genes involved in common pathways is helpful in understanding heterogeneous diseases.
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53 We have integrated the KEGG pathway mapping for gene variants, to explain/annotate variation.
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54
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55 This requires your VCF be annotated with either snpEff/VEP.
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56
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57 </help>
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58 <expand macro="citations"/>
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59 </tool>