Mercurial > repos > iuc > gemini_pathways

annotate gemini_pathways.xml @ 11:245d50e9ac22 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
author iuc
date Wed, 13 Jul 2022 15:01:24 +0000
parents 2220b0dc7d12
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
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2 <description>Map genes and variants to KEGG pathways</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>gemini_macros.xml</import>
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6 <token name="@BINARY@">pathways</token>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command>
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12 <![CDATA[
3
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13 @PROVIDE_ANNO_DATA@
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14
0
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15 gemini
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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="select"
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27 label="Version of ensembl genes to use"
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28 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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29 <option value="71">Ensembl 71</option>
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30 <option value="70">Ensembl 70</option>
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31 <option value="69">Ensembl 69</option>
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32 <option value="68">Ensembl 68</option>
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33 <option value="67">Ensembl 67</option>
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34 <option value="66">Ensembl 66</option>
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35 </param>
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36 <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False"
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37 label="Report only pathways with loss-of-function variants" help="(--lof)"/>
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38 <expand macro="annotation_dir" />
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39 </inputs>
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40 <outputs>
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41 <data name="outfile" format="tabular" />
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
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46 <param name="ensembl" value="71" />
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47 <output name="outfile">
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48 <assert_contents>
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49 <has_line_matching expression="chrom&#009;start&#009;end&#009;.*pathway.*" />
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50 </assert_contents>
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51 </output>
0
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52 </test>
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53 </tests>
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54 <help>
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55 **What it does**
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56
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57 Mapping genes to biological pathways is useful in understanding the function/role played by a gene.
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58 Likewise, genes involved in common pathways is helpful in understanding heterogeneous diseases.
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59 We have integrated the KEGG pathway mapping for gene variants, to explain/annotate variation.
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60
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61 This requires your VCF be annotated with either snpEff/VEP.
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63 </help>
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64 <expand macro="citations"/>
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65 </tool>