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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.misc.VcfFilterSequenceOntology" version="f21676175ed7d18ec569f34973dd2c03c23ab1e9" name="vcffilterso">
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3 <!--Date: 2015-02-27T15:54:06+01:00-->
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4 <description>Filter a VCF file annotated with SNPEff or VEP with terms from Sequence-Ontology</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__/vcffilterso.jar com.github.lindenb.jvarkit.tools.misc.VcfFilterSequenceOntology
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9 #for s in $accessions
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10 -A '$s'
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11 #end for
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12 $inverse $noreason -o ${output}.vcf.gz && mv ${output}.vcf.gz ${output} </command>
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13 <inputs>
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14 <param format="vcf" name="input" type="data" label="VCF input"/>
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15 <repeat name="accessions" title="accessions">
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16 <param name="acn" type="text" label="SO Accession Number">
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17 <validator type="regex" message="must match with SO:(number)">SO\:[0-9]+</validator>
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18 </param>
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19 </repeat>
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20 <param name="inverse" type="boolean" checked="false" label="inverse selection" truevalue="-v" falsevalue=""/>
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21 <param name="noreason" type="boolean" checked="false" label="disable reasoning" truevalue="-d" falsevalue=""/>
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22 </inputs>
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23 <outputs>
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24 <data format="vcf" name="output"/>
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25 </outputs>
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26 <stdio>
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27 <exit_code range="1:"/>
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28 <exit_code range=":-1"/>
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29 </stdio>
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30 <help>
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31
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32
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33 **Examples**
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34
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35
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36
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37
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38 **Inputs**
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39
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40
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41 - **VCF input** : VCF input
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42
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43 - **inverse selection** : inverse selection
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44
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45 - **disable reasoning** : disable reasoning
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46
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47
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48 **Outputs**
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49
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50
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51 - **output** : output
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52
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53
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54 **Wiki**
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55
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56 https://github.com/lindenb/jvarkit/wiki/VcfFilterSequenceOntology
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57
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58 -----
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59
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60
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61 **Author**
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62
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63 Pierre Lindenbaum PhD @yokofakun
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64
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65 **Citation**
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66
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67 If you use this Galaxy tool in work leading to a scientific publication please
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68 cite: Pierre Lindenbaum PhD https://github.com/lindenb/jvarkit
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69
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70 **Contribute**
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71
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72 - Issue Tracker: http://github.com/lindenb/jvarkit/issues`
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73 - Source Code: http://github.com/lindenb/jvarkit
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74
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75 **License**
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76
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77 The project is licensed under the MIT license.
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78
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79 **Compilation**
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80
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81 Date: 2015-02-27T15:54:06+01:00
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82 Version: f21676175ed7d18ec569f34973dd2c03c23ab1e9
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83 </help>
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84 </tool>
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