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1 <?xml version="1.0"?>
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2 <tool xmlns:date="http://exslt.org/dates-and-times" hidden="false" id="com.github.lindenb.jvarkit.tools.vcftrios.VCFTrios" version="f21676175ed7d18ec569f34973dd2c03c23ab1e9" name="vcftrio">
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3 <!--Date: 2015-02-27T15:54:05+01:00-->
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4 <description>Check for mendelian incompatibilities in a VCF</description>
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5 <requirements>
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6 <requirement type="binary">java</requirement>
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7 </requirements>
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8 <command>(gunzip -c ${input} || cat ${input}) | java -cp $__tool_directory__/commons-jexl-2.1.1.jar:$__tool_directory__/commons-logging-1.1.1.jar:$__tool_directory__/htsjdk-1.128.jar:$__tool_directory__/snappy-java-1.0.3-rc3.jar:$__tool_directory__/vcftrio.jar com.github.lindenb.jvarkit.tools.vcftrios.VCFTrios $filter -p $ped -o ${output}.vcf.gz && mv ${output}.vcf.gz ${output}</command>
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9 <inputs>
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10 <param format="vcf" name="input" type="data" label="VCF input"/>
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11 <param name="filter" type="boolean" checked="false" label="Create a FILTER in the FILTER column" truevalue="-f" falsevalue=""/>
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12 <param name="ped" type="data" format="tabular" label="Pedigree file (Family/name/father/mother/sex)"/>
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13 </inputs>
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14 <outputs>
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15 <data format="vcf" name="output"/>
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16 </outputs>
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17 <stdio>
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18 <exit_code range="1:"/>
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19 <exit_code range=":-1"/>
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20 </stdio>
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21 <help>
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22
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23 **Inputs**
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24
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25
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26 - **VCF input** : VCF input
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27
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28 - **Create a FILTER in the FILTER column** : Create a FILTER in the FILTER column
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29
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30 - **Pedigree file (Family/name/father/mother/sex)** : Pedigree file (Family/name/father/mother/sex)
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31
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32
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33 **Outputs**
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34
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35
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36 - **output** : output
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37
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38
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39 **Wiki**
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40
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41 https://github.com/lindenb/jvarkit/wiki/VCFTrio
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42
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43 -----
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44
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45
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46 **Author**
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47
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48 Pierre Lindenbaum PhD @yokofakun
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49
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50 **Citation**
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51
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52 If you use this Galaxy tool in work leading to a scientific publication please
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53 cite: Pierre Lindenbaum PhD https://github.com/lindenb/jvarkit
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54
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55 **Contribute**
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56
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57 - Issue Tracker: http://github.com/lindenb/jvarkit/issues`
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58 - Source Code: http://github.com/lindenb/jvarkit
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59
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60 **License**
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61
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62 The project is licensed under the MIT license.
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63
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64 **Compilation**
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65
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66 Date: 2015-02-27T15:54:05+01:00
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67 Version: f21676175ed7d18ec569f34973dd2c03c23ab1e9
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68 </help>
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69 </tool>
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