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1 <tool id="gemini_recessive_and_dominant" name="GEMINI autosomal recessive/dominant" version="@VERSION@.0">
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2 <description>Find variants meeting an autosomal recessive/dominant model</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 </macros>
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8 <command>
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9 <![CDATA[
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10 gemini
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11
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12 #if $rec_or_dom == 'recessive':
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13 ## start autosomal_recessive
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14 autosomal_recessive
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15 #else:
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16 ## start autosomal_dominant
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17 autosomal_dominant
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18 #end if
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19
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20 #if $report.report_selector != 'all':
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21 --columns "${report.columns}"
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22 #end if
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23
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24 #if $filter.filter_selector == 'yes':
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25 --filter "${filter.filter}"
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26 #end if
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27
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28 -d $d
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29 #if int($min_kindreds) > 0:
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30 --min-kindreds $min_kindreds
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31 #end if
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32
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33 "${ infile }"
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34 > "${ outfile }"
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35 ]]>
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36 </command>
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37 <expand macro="stdio" />
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38 <inputs>
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39
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40 <param name="rec_or_dom" type="select" label="Autosomal ..." help="">
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41 <option value="recessive">recessive</option>
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42 <option value="dominant">dominant</option>
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43 </param>
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44
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45 <param name="infile" type="data" format="sqlite" label="GEMINI database" />
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46 <expand macro="column_filter" />
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47 <expand macro="filter" />
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48 <expand macro="min_sequence_depth" />
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49 <param name="min_kindreds" size="4" type="integer" value="-1" lebel="The min. number of kindreds that must have a candidate variant in a gene"
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50 help="-1 means default values (--min-kindreds)" />
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51
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52 </inputs>
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53 <outputs>
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54 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
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55 </outputs>
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56 <tests>
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57 <test>
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58 </test>
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59 </tests>
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60 <help>
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61 **What it does**
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62
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63 Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI, one can leverage a
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64 built-in tool for identifying variants that meet an autosomal recessive or dominant inheritance pattern.
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65 The reported variants will be restricted to those variants having the potential to impact the function of affecting protein coding transcripts.
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66
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67 @CITATION@
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68 </help>
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69 <expand macro="citations"/>
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70 </tool>
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