Mercurial > repos > devteam > vcffilter

annotate vcffilter.xml @ 9:4cb86a8987de draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit f28d66c0bcad8ac29be2afec28bc639317239775
author iuc
date Tue, 01 Oct 2024 13:48:03 +0000
parents af9bfb0f213e
children
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7ce3b93e0883 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
parents: 6
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1 <tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy3">
1
eac1f91d50b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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2 <description>filter VCF data in a variety of attributes</description>
eac1f91d50b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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3 <macros>
eac1f91d50b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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4 <import>macros.xml</import>
eac1f91d50b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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5 </macros>
eac1f91d50b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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6 <expand macro="requirements">
8
af9bfb0f213e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 36e9065027cc7bf721e9d203208477ee88906c57"
iuc
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7 <requirement type="package" version="1.10.2">htslib</requirement>
1
eac1f91d50b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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8 </expand>
eac1f91d50b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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9 <expand macro="stdio" />
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iuc
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10 <command><![CDATA[
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
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11 ln -s '$input1' input1.vcf &&
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
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12 bgzip input1.vcf &&
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
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13 tabix -p vcf input1.vcf.gz &&
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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14 vcffilter
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
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15 #for $filter_el in $filter_repeat:
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
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16 $filter_el.filter_type '$filter_el.filter_value'
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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17 #end for
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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18 $filter_sites
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
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19 $tag_pass
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
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20 $tag_fail
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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21 $append_filter
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
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22 $allele_tag
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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23 $invert
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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24 $or
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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25 #if str($region):
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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26 --region '$region'
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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27 #end if
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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28 input1.vcf.gz
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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29 > '${out_file1}'
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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30 ]]></command>
1
eac1f91d50b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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31 <inputs>
3
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32 <param name="input1" type="data" format="vcf" label="VCF dataset to filter"/>
4
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33 <repeat name="filter_repeat" title="more filters" min="1">
3
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34 <param name="filter_type" type="select" label="Select the filter type">
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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35 <option value="-f">Info filter (-f)</option>
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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36 <option value="-g">Genotype filter (-g)</option>
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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37 </param>
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7ce3b93e0883 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
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38 <param name="filter_value" type="text" value="DP &gt; 10" label="Specify filtering value" help="See explanation of filtering options below">
3
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39 <sanitizer>
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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40 <valid initial="string.printable">
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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41 <remove value="&apos;"/>
4
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42 <remove value="&quot;"/>
3
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43 </valid>
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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44 <mapping initial="none">
4
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45 <add source="&apos;" target=""/>
763f297f3272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
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46 <add source="&quot;" target=""/>
3
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47 </mapping>
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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48 </sanitizer>
7
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49 <validator type="expression" message="Invalid operator provided, valid operators are =, !, &lt;, &gt;, |, &amp;.">value is not None and not any(x in value for x in ["&lt;=", "=&lt;", "&gt;=", "=&gt;"])</validator>
3
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50 </param>
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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51 </repeat>
9
4cb86a8987de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit f28d66c0bcad8ac29be2afec28bc639317239775
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52 <param argument="--filter-sites" type="boolean" truevalue="--filter-sites" falsevalue="" label="Filter entire records, not just alleles"/>
4cb86a8987de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit f28d66c0bcad8ac29be2afec28bc639317239775
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53 <param argument="--tag-pass" type="boolean" truevalue="--tag-pass" falsevalue="" label="Tag vcf records as positively filtered with this tag, print all records"/>
4cb86a8987de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit f28d66c0bcad8ac29be2afec28bc639317239775
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54 <param argument="--tag-fail" type="boolean" truevalue="--tag-fail" falsevalue="" label="Tag vcf records as negatively filtered with this tag, print all records"/>
4cb86a8987de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit f28d66c0bcad8ac29be2afec28bc639317239775
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55 <param argument="--append-filter" type="boolean" truevalue="--append-filter" falsevalue="" label="Append the existing filter tag, don't just replace it"/>
4cb86a8987de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit f28d66c0bcad8ac29be2afec28bc639317239775
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56 <param argument="--allele-tag" type="boolean" truevalue="--allele-tag" falsevalue="" label="Apply --tag-pass on a per-allele basis, adds or sets the corresponding INFO field tag"/>
3
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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57 <param argument="--invert" type="boolean" truevalue="--invert" falsevalue="" label="Inverts the filter, e.g. grep -v"/>
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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58 <param argument="--or" type="boolean" truevalue="--or" falsevalue="" label="Use logical OR instead of AND to combine filters"/>
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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59 <param argument="--region" type="text" label="Specify a region on which to target the filtering" help="Regions should be specified as chr:start-end, e.g X:1000-2000"/>
1
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60 </inputs>
eac1f91d50b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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61 <outputs>
3
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62 <data name="out_file1" format="vcf" />
1
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63 </outputs>
eac1f91d50b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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64 <tests>
eac1f91d50b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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65 <test>
3
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66 <param name="filter_repeat_0|filter_type" value="-f"/>
f1f4cb7e7bb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
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67 <param name="filter_repeat_0|filter_value" value="DP &gt; 10"/>
1
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68 <param name="input1" value="vcflib.vcf"/>
eac1f91d50b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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69 <output name="out_file1" file="vcffilter-test1.vcf"/>
eac1f91d50b1 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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70 </test>
7
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71 <test>
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72 <param name="filter_repeat_0|filter_type" value="-f"/>
7ce3b93e0883 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
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73 <param name="filter_repeat_0|filter_value" value="!( DP &gt; 10 )"/>
7ce3b93e0883 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
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74 <param name="invert" value="true"/>
7ce3b93e0883 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
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75 <param name="input1" value="vcflib.vcf"/>
7ce3b93e0883 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
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76 <output name="out_file1" file="vcffilter-test2.vcf"/>
7ce3b93e0883 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
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77 </test>
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78 </tests>
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79 <help><![CDATA[
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80 You can specify the following options within the **Specify filtering expression** box in any combination::
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81
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82 -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter
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83 -g, --genotype-filter specifies a filter to apply to the genotype fields of records
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84 -s, --filter-sites filter entire records, not just alleles
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85 -t, --tag-pass tag vcf records as positively filtered with this tag, print all records
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86 -F, --tag-fail tag vcf records as negatively filtered with this tag, print all records
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87 -A, --append-filter append the existing filter tag, don't just replace it
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88 -a, --allele-tag apply -t on a per-allele basis. adds or sets the corresponding INFO field tag
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89 -v, --invert inverts the filter, e.g. grep -v
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90 -o, --or use logical OR instead of AND to combine filters
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91 -r, --region specify a region on which to target the filtering (must be used in conjunction with -f or -g)
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92
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93 To specify filters, click on the 'Insert Add filters' button, choose a filter type
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94 (e.g., 'Info filter' or 'Genotype filter'), and specify filter value according to the
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95 following pattern::
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96
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97 - For 'Info filter (-f)':: {ID} {operator} {value}
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98 For instance:: DP > 10
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99
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100 - For 'Genotype fields (-g)':: {ID} {operator} {value}
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101 For instance:: GT = 1|1
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102
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103 - For 'Flag' fields (when 'Info filter (-f)' is selected for filter type field):: {value}
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104 For instance:: CpG
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105
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106 Any number of filters may be specified. They are combined via logical AND unless the --or option is specified. For convenience, you can specify "QUAL" to refer to the quality of the site, even though it does not appear in the INFO fields.
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107
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108 Operators can be any of::
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109
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110 =, !, <, >, |, &
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111
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112 Obtain logical negation through the use of parentheses, e.g. "! ( DP = 10 )"
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113 Please mind the blank space between parentheses and the arguments.
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114
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115 To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f)::
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116
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117 -r chr20:14000-15000 # only output calls between positions 14,000 and 15,000 on chromosome 20
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118 -r chrX # only output call on chromosome X
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119
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120 -----
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121
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122 Vcffilter @IS_PART_OF_VCFLIB@
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123 ]]></help>
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124 <expand macro="citations" />
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125 </tool>