# HG changeset patch # User iuc # Date 1546109816 18000 # Node ID 763f297f327209062bf36e1b0dcad5f5514bdf6e # Parent f1f4cb7e7bb76256bd392f574903fc4afd0c6a71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26 diff -r f1f4cb7e7bb7 -r 763f297f3272 vcffilter.xml --- a/vcffilter.xml Mon Mar 26 10:21:13 2018 -0400 +++ b/vcffilter.xml Sat Dec 29 13:56:56 2018 -0500 @@ -1,4 +1,4 @@ - + filter VCF data in a variety of attributes macros.xml @@ -30,7 +30,7 @@ ]]> - + @@ -39,9 +39,11 @@ + - + + @@ -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.