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comparison vcffilter.xml @ 5:de885f4afb7f draft

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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
comparison
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4:6b935ab36d7b 5:de885f4afb7f
1 <tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy1"> 1 <tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy2">
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">
28 input1.vcf.gz 28 input1.vcf.gz
29 > '${out_file1}' 29 > '${out_file1}'
30 ]]></command> 30 ]]></command>
31 <inputs> 31 <inputs>
32 <param name="input1" type="data" format="vcf" label="VCF dataset to filter"/> 32 <param name="input1" type="data" format="vcf" label="VCF dataset to filter"/>
33 <repeat name="filter_repeat" title="Add filters"> 33 <repeat name="filter_repeat" title="more filters" min="1">
34 <param name="filter_type" type="select" label="Select the filter type"> 34 <param name="filter_type" type="select" label="Select the filter type">
35 <option value="-f">Info filter (-f)</option> 35 <option value="-f">Info filter (-f)</option>
36 <option value="-g">Genotype filter (-g)</option> 36 <option value="-g">Genotype filter (-g)</option>
37 </param> 37 </param>
38 <param name="filter_value" type="text" value="DP &gt; 10" label="Specify filterting value" help="See explanation of filtering options below"> 38 <param name="filter_value" type="text" value="DP &gt; 10" label="Specify filterting value" help="See explanation of filtering options below">
39 <sanitizer> 39 <sanitizer>
40 <valid initial="string.printable"> 40 <valid initial="string.printable">
41 <remove value="&apos;"/> 41 <remove value="&apos;"/>
42 <remove value="&quot;"/>
42 </valid> 43 </valid>
43 <mapping initial="none"> 44 <mapping initial="none">
44 <add source="&apos;" target="__sq__"/> 45 <add source="&apos;" target=""/>
46 <add source="&quot;" target=""/>
45 </mapping> 47 </mapping>
46 </sanitizer> 48 </sanitizer>
47 </param> 49 </param>
48 </repeat> 50 </repeat>
49 <param name="filter_sites" argument="--filter-sites" type="boolean" truevalue="--filter-sites" falsevalue="" label="Filter entire records, not just alleles"/> 51 <param name="filter_sites" argument="--filter-sites" type="boolean" truevalue="--filter-sites" falsevalue="" label="Filter entire records, not just alleles"/>
78 -a, --allele-tag apply -t on a per-allele basis. adds or sets the corresponding INFO field tag 80 -a, --allele-tag apply -t on a per-allele basis. adds or sets the corresponding INFO field tag
79 -v, --invert inverts the filter, e.g. grep -v 81 -v, --invert inverts the filter, e.g. grep -v
80 -o, --or use logical OR instead of AND to combine filters 82 -o, --or use logical OR instead of AND to combine filters
81 -r, --region specify a region on which to target the filtering (must be used in conjunction with -f or -g) 83 -r, --region specify a region on which to target the filtering (must be used in conjunction with -f or -g)
82 84
83 Filters are specified in the form {ID} {operator} {value}:: 85 To specify filters, click on the 'Insert Add filters' button, choose a filter type
86 (e.g., 'Info filter' or 'Genotype filter'), and specify filter value according to the
87 following pattern::
84 88
85 -f "DP > 10" # for info fields 89 - For 'Info filter (-f)':: {ID} {operator} {value}
86 -g "GT = 1|1" # for genotype fields 90 For instance:: DP > 10
87 -f "CpG" # for 'flag' fields 91
92 - For 'Genotype fields (-g)':: {ID} {operator} {value}
93 For instance:: GT = 1|1
94
95 - For 'Flag' fields (when 'Info filter (-f)' is selected for filter type field):: {value}
96 For instance:: CpG
88 97
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. 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.
90 99
91 Operators can be any of:: 100 Operators can be any of::
92 101