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comparison vcffilter.xml @ 3:f1f4cb7e7bb7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit bd03161519b5a55c4395ae9715688799319427b2
author iuc
date Mon, 26 Mar 2018 10:21:13 -0400
parents db6fd4b2a697
children 763f297f3272
comparison
equal deleted inserted replaced
2:db6fd4b2a697 3:f1f4cb7e7bb7
1 <tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@.0"> 1 <tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy1">
2 <description>filter VCF data in a variety of attributes</description> 2 <description>filter VCF data in a variety of attributes</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="1.3">htslib</requirement> 7 <requirement type="package" version="1.7">htslib</requirement>
8 </expand> 8 </expand>
9 <expand macro="stdio" /> 9 <expand macro="stdio" />
10 <command> 10 <command><![CDATA[
11 <!-- This tools depends on tabix functionality, which is currently distributed with Galaxy itself via a pysam egg --> 11 ln -s '$input1' input1.vcf &&
12 ln -s "${input1}" input1.vcf &amp;&amp; 12 bgzip input1.vcf &&
13 bgzip input1.vcf &amp;&amp; 13 tabix -p vcf input1.vcf.gz &&
14 tabix -p vcf input1.vcf.gz &amp;&amp; 14 vcffilter
15 vcffilter ${filterList} input1.vcf.gz > "${out_file1}" 15 #for $filter_el in $filter_repeat:
16 </command> 16 $filter_el.filter_type '$filter_el.filter_value'
17 17 #end for
18 $filter_sites
19 $tag_pass
20 $tag_fail
21 $append_filter
22 $allele_tag
23 $invert
24 $or
25 #if str($region):
26 --region '$region'
27 #end if
28 input1.vcf.gz
29 > '${out_file1}'
30 ]]></command>
18 <inputs> 31 <inputs>
19 <param name="filterList" type="text" value="-f &quot;DP &gt; 10&quot;" label="Specify filterting expression" help="See explanation of filtering options below"> 32 <param name="input1" type="data" format="vcf" label="VCF dataset to filter"/>
20 <sanitizer> 33 <repeat name="filter_repeat" title="Add filters">
21 <valid initial="string.printable"> 34 <param name="filter_type" type="select" label="Select the filter type">
22 <remove value="&apos;"/> 35 <option value="-f">Info filter (-f)</option>
23 </valid> 36 <option value="-g">Genotype filter (-g)</option>
24 <mapping initial="none"> 37 </param>
25 <add source="&apos;" target="__sq__"/> 38 <param name="filter_value" type="text" value="DP &gt; 10" label="Specify filterting value" help="See explanation of filtering options below">
26 </mapping> 39 <sanitizer>
27 </sanitizer> 40 <valid initial="string.printable">
28 </param> 41 <remove value="&apos;"/>
29 <param format="vcf" name="input1" type="data" label="VCF dataset to filter"/> 42 </valid>
43 <mapping initial="none">
44 <add source="&apos;" target="__sq__"/>
45 </mapping>
46 </sanitizer>
47 </param>
48 </repeat>
49 <param name="filter_sites" argument="--filter-sites" type="boolean" truevalue="--filter-sites" falsevalue="" label="Filter entire records, not just alleles"/>
50 <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"/>
51 <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"/>
52 <param name="append_filter" argument="--append-filter" type="boolean" truevalue="--append-filter" falsevalue="" label="Append the existing filter tag, don't just replace it"/>
53 <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"/>
54 <param argument="--invert" type="boolean" truevalue="--invert" falsevalue="" label="Inverts the filter, e.g. grep -v"/>
55 <param argument="--or" type="boolean" truevalue="--or" falsevalue="" label="Use logical OR instead of AND to combine filters"/>
56 <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"/>
30 </inputs> 57 </inputs>
31 <outputs> 58 <outputs>
32 <data format="vcf" name="out_file1" /> 59 <data name="out_file1" format="vcf" />
33 </outputs> 60 </outputs>
34 <tests> 61 <tests>
35 <test> 62 <test>
36 <param name="filterList" value="-f &quot;DP &gt; 10&quot;"/> 63 <param name="filter_repeat_0|filter_type" value="-f"/>
64 <param name="filter_repeat_0|filter_value" value="DP &gt; 10"/>
37 <param name="input1" value="vcflib.vcf"/> 65 <param name="input1" value="vcflib.vcf"/>
38 <output name="out_file1" file="vcffilter-test1.vcf"/> 66 <output name="out_file1" file="vcffilter-test1.vcf"/>
39 </test> 67 </test>
40 </tests> 68 </tests>
41 <help> 69 <help><![CDATA[
42 You can specify the following options within the **Specify filtering expression** box in any combination:: 70 You can specify the following options within the **Specify filtering expression** box in any combination::
43 71
44 -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter 72 -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter
45 -g, --genotype-filter specifies a filter to apply to the genotype fields of records 73 -g, --genotype-filter specifies a filter to apply to the genotype fields of records
46 -s, --filter-sites filter entire records, not just alleles 74 -s, --filter-sites filter entire records, not just alleles
58 -g "GT = 1|1" # for genotype fields 86 -g "GT = 1|1" # for genotype fields
59 -f "CpG" # for 'flag' fields 87 -f "CpG" # for 'flag' fields
60 88
61 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. 89 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.
62 90
63 Operators can be any of: =, !, &lt;, &gt;, pipe, &amp; 91 Operators can be any of::
64 92
93 =, !, <, >, |, &
65 94
66 To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f):: 95 To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f)::
67 96
68 -r chr20:14000-15000 # only output calls between positions 14,000 and 15,000 on chromosome 20 97 -r chr20:14000-15000 # only output calls between positions 14,000 and 15,000 on chromosome 20
69 -r chrX # only output call on chromosome X 98 -r chrX # only output call on chromosome X
70 99
71 ----- 100 -----
72 101
73 Vcffilter @IS_PART_OF_VCFLIB@ 102 Vcffilter @IS_PART_OF_VCFLIB@
74 </help> 103 ]]></help>
75 <expand macro="citations" /> 104 <expand macro="citations" />
76 </tool> 105 </tool>