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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
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2 <description>Find genes among variants that are interacting partners</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@">interactions</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 #if $gene.gene_selector == 'lof':
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14 ## lof interactions is a separate program
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15 lof_interactions
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16 #else:
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17 ## use normal gemini interactions program
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18 @BINARY@
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19 -g "${gene.gene}"
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20 #end if
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21
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22 -r "${radius}"
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23 $variant_mode
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24 "${ infile }"
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25 > "${ outfile }"
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26 ]]>
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27 </command>
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28 <expand macro="stdio" />
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29 <inputs>
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30 <param name="infile" type="data" format="sqlite" label="GEMINI database" />
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31
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32 <conditional name="gene">
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33 <param name="gene_selector" type="select" label="Studying" help="">
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34 <option value="gene">Interesting gene</option>
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35 <option value="lof">All loss-of-function variants</option>
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36 </param>
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37 <when value="gene">
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38 <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (-g)" />
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39 </when>
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40 <when value="lof"/>
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41 </conditional>
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42 <expand macro="annotation_dir" />
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43 <expand macro="radius" />
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44 <expand macro="variant_mode" />
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45 </inputs>
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46 <outputs>
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47 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
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48 </outputs>
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49 <tests>
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50 <test>
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51 </test>
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52 </tests>
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53 <help>
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54 **What it does**
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55
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56 Integrating the knowledge of the known protein-protein interactions would be useful in explaining variation data.
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57 Meaning to say that a damaging variant in an interacting partner of a potential protein may be equally interesting as the
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58 protein itself. We have used the HPRD_ binary interaction data to build a p-p network graph which can be explored by GEMINI.
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59
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60 .. _HPRD: http://www.ncbi.nlm.nih.gov/pubmed/18988627
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61
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62
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63 @CITATION@
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64 </help>
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65 <expand macro="citations">
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66 <citation type="doi">10.1093/nar/gkn892</citation><!-- HPRD citation -->
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67 </expand>
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68 </tool>
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