annotate vcffilter.xml @ 5:de885f4afb7f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
author iuc
date Sat, 29 Dec 2018 13:57:17 -0500
parents 6b935ab36d7b
children 9442e22779ca
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
de885f4afb7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
iuc
parents: 4
diff changeset
1 <tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy2">
2
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
2 <description>filter VCF data in a variety of attributes</description>
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
3 <macros>
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
4 <import>macros.xml</import>
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
5 </macros>
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
6 <expand macro="requirements">
4
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
7 <requirement type="package" version="1.7">htslib</requirement>
2
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
8 </expand>
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
9 <expand macro="stdio" />
4
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
10 <command><![CDATA[
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
11 ln -s '$input1' input1.vcf &&
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
12 bgzip input1.vcf &&
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
13 tabix -p vcf input1.vcf.gz &&
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
14 vcffilter
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
15 #for $filter_el in $filter_repeat:
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
16 $filter_el.filter_type '$filter_el.filter_value'
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
17 #end for
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
18 $filter_sites
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
19 $tag_pass
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
20 $tag_fail
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
21 $append_filter
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
22 $allele_tag
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
23 $invert
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
24 $or
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
25 #if str($region):
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
26 --region '$region'
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
27 #end if
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
28 input1.vcf.gz
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
29 > '${out_file1}'
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
30 ]]></command>
2
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
31 <inputs>
4
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
32 <param name="input1" type="data" format="vcf" label="VCF dataset to filter"/>
5
de885f4afb7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
iuc
parents: 4
diff changeset
33 <repeat name="filter_repeat" title="more filters" min="1">
4
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
34 <param name="filter_type" type="select" label="Select the filter type">
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
35 <option value="-f">Info filter (-f)</option>
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
36 <option value="-g">Genotype filter (-g)</option>
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
37 </param>
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
38 <param name="filter_value" type="text" value="DP &gt; 10" label="Specify filterting value" help="See explanation of filtering options below">
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
39 <sanitizer>
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
40 <valid initial="string.printable">
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
41 <remove value="&apos;"/>
5
de885f4afb7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
iuc
parents: 4
diff changeset
42 <remove value="&quot;"/>
4
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
43 </valid>
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
44 <mapping initial="none">
5
de885f4afb7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
iuc
parents: 4
diff changeset
45 <add source="&apos;" target=""/>
de885f4afb7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
iuc
parents: 4
diff changeset
46 <add source="&quot;" target=""/>
4
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
47 </mapping>
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
48 </sanitizer>
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
49 </param>
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
50 </repeat>
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
51 <param name="filter_sites" argument="--filter-sites" type="boolean" truevalue="--filter-sites" falsevalue="" label="Filter entire records, not just alleles"/>
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
52 <param name="tag_pass" argument="--tag-pass" type="boolean" truevalue="--tag-pass" falsevalue="" label="Tag vcf records as positively filtered with this tag, print all records"/>
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
53 <param name="tag_fail" argument="--tag-fail" type="boolean" truevalue="--tag-fail" falsevalue="" label="Tag vcf records as negatively filtered with this tag, print all records"/>
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
54 <param name="append_filter" argument="--append-filter" type="boolean" truevalue="--append-filter" falsevalue="" label="Append the existing filter tag, don't just replace it"/>
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
55 <param name="allele_tag" 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"/>
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
56 <param argument="--invert" type="boolean" truevalue="--invert" falsevalue="" label="Inverts the filter, e.g. grep -v"/>
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
57 <param argument="--or" type="boolean" truevalue="--or" falsevalue="" label="Use logical OR instead of AND to combine filters"/>
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
58 <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"/>
2
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
59 </inputs>
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
60 <outputs>
4
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
61 <data name="out_file1" format="vcf" />
2
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
62 </outputs>
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
63 <tests>
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
64 <test>
4
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
65 <param name="filter_repeat_0|filter_type" value="-f"/>
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
66 <param name="filter_repeat_0|filter_value" value="DP &gt; 10"/>
2
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
67 <param name="input1" value="vcflib.vcf"/>
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
68 <output name="out_file1" file="vcffilter-test1.vcf"/>
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
69 </test>
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
70 </tests>
4
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
71 <help><![CDATA[
2
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
72 You can specify the following options within the **Specify filtering expression** box in any combination::
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
73
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
74 -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
75 -g, --genotype-filter specifies a filter to apply to the genotype fields of records
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
76 -s, --filter-sites filter entire records, not just alleles
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
77 -t, --tag-pass tag vcf records as positively filtered with this tag, print all records
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
78 -F, --tag-fail tag vcf records as negatively filtered with this tag, print all records
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
79 -A, --append-filter append the existing filter tag, don't just replace it
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
80 -a, --allele-tag apply -t on a per-allele basis. adds or sets the corresponding INFO field tag
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
81 -v, --invert inverts the filter, e.g. grep -v
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
82 -o, --or use logical OR instead of AND to combine filters
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
83 -r, --region specify a region on which to target the filtering (must be used in conjunction with -f or -g)
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
84
5
de885f4afb7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
iuc
parents: 4
diff changeset
85 To specify filters, click on the 'Insert Add filters' button, choose a filter type
de885f4afb7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
iuc
parents: 4
diff changeset
86 (e.g., 'Info filter' or 'Genotype filter'), and specify filter value according to the
de885f4afb7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
iuc
parents: 4
diff changeset
87 following pattern::
2
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
88
5
de885f4afb7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
iuc
parents: 4
diff changeset
89 - For 'Info filter (-f)':: {ID} {operator} {value}
de885f4afb7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
iuc
parents: 4
diff changeset
90 For instance:: DP > 10
de885f4afb7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
iuc
parents: 4
diff changeset
91
de885f4afb7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
iuc
parents: 4
diff changeset
92 - For 'Genotype fields (-g)':: {ID} {operator} {value}
de885f4afb7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
iuc
parents: 4
diff changeset
93 For instance:: GT = 1|1
de885f4afb7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
iuc
parents: 4
diff changeset
94
de885f4afb7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
iuc
parents: 4
diff changeset
95 - For 'Flag' fields (when 'Info filter (-f)' is selected for filter type field):: {value}
de885f4afb7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
iuc
parents: 4
diff changeset
96 For instance:: CpG
2
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
97
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
98 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.
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
99
4
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
100 Operators can be any of::
2
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
101
4
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
102 =, !, <, >, |, &
2
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
103
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
104 To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f)::
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
105
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
106 -r chr20:14000-15000 # only output calls between positions 14,000 and 15,000 on chromosome 20
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
107 -r chrX # only output call on chromosome X
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
108
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
109 -----
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
110
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
111 Vcffilter @IS_PART_OF_VCFLIB@
4
6b935ab36d7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
iuc
parents: 3
diff changeset
112 ]]></help>
2
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
113 <expand macro="citations" />
2d3c06c7e1f9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
parents: 1
diff changeset
114 </tool>