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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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11
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12 #if str($rec_or_dom) == 'recessive':
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13 ## start autosomal_recessive
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14 autosomal_recessive
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15 #else:
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16 ## start autosomal_dominant
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17 autosomal_dominant
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18 #end if
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19
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20 #if str($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 @CMDLN_SQL_FILTER_FILTER_OPTION@
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25
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26 -d $d
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27 #if int($min_kindreds) > 0:
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28 --min-kindreds $min_kindreds
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29 #end if
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30
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31 "${ infile }"
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32 > "${ outfile }"
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33 ]]>
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34 </command>
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35 <expand macro="stdio" />
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36 <inputs>
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37
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38 <param name="rec_or_dom" type="select" label="Autosomal ..." help="">
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39 <option value="recessive">recessive</option>
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40 <option value="dominant">dominant</option>
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41 </param>
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42
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43 <expand macro="infile" />
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44 <expand macro="column_filter" />
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45 <expand macro="filter" />
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46 <expand macro="min_sequence_depth" />
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47 <param name="min_kindreds" size="4" type="integer" value="-1" label="The min. number of kindreds that must have a candidate variant in a gene"
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48 help="-1 means default values (--min-kindreds)" />
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49
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50 </inputs>
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51 <outputs>
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52 <data name="outfile" format="tabular" />
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53 </outputs>
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54 <tests>
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55 <test>
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56 </test>
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57 </tests>
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58 <help>
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59 **What it does**
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60
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61 Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI, one can leverage a
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62 built-in tool for identifying variants that meet an autosomal recessive or dominant inheritance pattern.
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63 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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64
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65 @CITATION@
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66 </help>
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67 <expand macro="citations"/>
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68 </tool>
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