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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
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2 <description>Identifying potential de novo mutations</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@">de_novo</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 @BINARY@
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12
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13 #if $report.report_selector != 'all':
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14 --columns "${report.columns}"
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15 #end if
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16
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4
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17 @CMDLN_SQL_FILTER_FILTER_OPTION@
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18
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19 -d $d
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20 "${ infile }"
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21 > "${ outfile }"
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22 ]]>
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23 </command>
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24 <expand macro="stdio" />
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25 <inputs>
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2
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26 <expand macro="infile" />
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0
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27
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28 <expand macro="column_filter" />
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29 <expand macro="filter" />
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30 <expand macro="min_sequence_depth" />
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31 </inputs>
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32 <outputs>
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2
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33 <data name="outfile" format="tabular" />
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0
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34 </outputs>
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35 <tests>
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36 <test>
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37 </test>
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38 </tests>
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39 <help>
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40 **What it does**
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41
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42 Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI,
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43 you can use this tool for identifying de novo (a.k.a spontaneous) mutations that arise in offspring.
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44
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45 @CITATION@
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46 </help>
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47 <expand macro="citations"/>
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48 </tool>
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