Mercurial > repos > devteam > vcffilter
changeset 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 |
files | vcffilter.xml |
diffstat | 1 files changed, 16 insertions(+), 7 deletions(-) [+] |
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--- a/vcffilter.xml Mon Mar 26 10:21:29 2018 -0400 +++ b/vcffilter.xml Sat Dec 29 13:57:17 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy1"> +<tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy2"> <description>filter VCF data in a variety of attributes</description> <macros> <import>macros.xml</import> @@ -30,7 +30,7 @@ ]]></command> <inputs> <param name="input1" type="data" format="vcf" label="VCF dataset to filter"/> - <repeat name="filter_repeat" title="Add filters"> + <repeat name="filter_repeat" title="more filters" min="1"> <param name="filter_type" type="select" label="Select the filter type"> <option value="-f">Info filter (-f)</option> <option value="-g">Genotype filter (-g)</option> @@ -39,9 +39,11 @@ <sanitizer> <valid initial="string.printable"> <remove value="'"/> + <remove value="""/> </valid> <mapping initial="none"> - <add source="'" target="__sq__"/> + <add source="'" target=""/> + <add source=""" target=""/> </mapping> </sanitizer> </param> @@ -80,11 +82,18 @@ -o, --or use logical OR instead of AND to combine filters -r, --region specify a region on which to target the filtering (must be used in conjunction with -f or -g) -Filters are specified in the form {ID} {operator} {value}:: +To specify filters, click on the 'Insert Add filters' button, choose a filter type +(e.g., 'Info filter' or 'Genotype filter'), and specify filter value according to the +following pattern:: - -f "DP > 10" # for info fields - -g "GT = 1|1" # for genotype fields - -f "CpG" # for 'flag' fields +- For 'Info filter (-f)':: {ID} {operator} {value} + For instance:: DP > 10 + +- For 'Genotype fields (-g)':: {ID} {operator} {value} + For instance:: GT = 1|1 + +- For 'Flag' fields (when 'Info filter (-f)' is selected for filter type field):: {value} + For instance:: CpG 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.