Mercurial > repos > devteam > vcftools_annotate
changeset 6:a6e0edfcfdae draft default tip
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:59:18 -0400 |
| parents | 01bb3234beb9 |
| children | |
| files | tool_dependencies.xml vcftools_annotate.xml |
| diffstat | 2 files changed, 10 insertions(+), 4 deletions(-) [+] |
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--- a/tool_dependencies.xml Sun Nov 24 10:56:14 2013 -0500 +++ b/tool_dependencies.xml Tue Oct 13 12:59:18 2015 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="vcftools" version="0.1.11"> - <repository changeset_revision="4081df719fff" name="package_vcftools_0_1_11" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="4081df719fff" name="package_vcftools_0_1_11" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>
--- a/vcftools_annotate.xml Sun Nov 24 10:56:14 2013 -0500 +++ b/vcftools_annotate.xml Tue Oct 13 12:59:18 2015 -0400 @@ -1,5 +1,5 @@ <tool id="vcftools_annotate" name="Annotate" version="0.1"> - <description>a VCF dataset with filters</description> + <description>a VCF dataset with custom filters</description> <requirements> <requirement type="binary">echo</requirement> @@ -47,8 +47,14 @@ </tests> <help> - Please see the VCFtools `documentation`__ for help and further information. +Annotates VCF dataset with custom annotations. For example, if this format tag is used for allele frequency: + +##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency"> - .. __: http://vcftools.sourceforge.net/docs.html +you can add a filter for allele frequency using "FORMAT/FREQ" as the tag name and the condition ">= [desired allele freq]" + +Please see the VCFtools `documentation`__ for help and further information. + +.. __: http://vcftools.sourceforge.net/perl_module.html#vcf-annotate </help> </tool>