Mercurial > repos > iuc > bcftools_norm
changeset 11:67e2bd1c4579 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 7ea221c576832871e9e5876d6927887d567d4f98"
| author | iuc |
|---|---|
| date | Thu, 28 Nov 2019 10:05:48 -0500 |
| parents | da6fc9f4a367 |
| children | a62e934346f5 |
| files | bcftools_norm.xml |
| diffstat | 1 files changed, 15 insertions(+), 1 deletions(-) [+] |
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--- a/bcftools_norm.xml Thu Oct 17 02:52:10 2019 -0400 +++ b/bcftools_norm.xml Thu Nov 28 10:05:48 2019 -0500 @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1"> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy2"> <description>Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows</description> <macros> <token name="@EXECUTABLE@">norm</token> @@ -7,6 +7,9 @@ </macros> <expand macro="requirements"> <expand macro="samtools_requirement"/> + <!-- gawk only required for current bcftools norm bug workaround + Remove once fixed (see command section below --> + <requirement type="package" version="5.0.1">gawk</requirement> </expand> <expand macro="version_command" /> <command detect_errors="aggressive"><![CDATA[ @@ -14,6 +17,17 @@ @PREPARE_INPUT_FILE@ #set $section = $reference_source @PREPARE_FASTA_REF@ + +## The next two lines are a workaround for a bug in bcftools norm up to version +## 1.9, which caused indel normalization to be case-sensitive +## see: +## https://github.com/samtools/bcftools/commit/65b211da1f5cdbf1c7c11eb610481a736fa88bda +## https://github.com/samtools/bcftools/commit/77b0a27a156803e382d60651ff94ea0bd95fad0f +## With the next release of bcftools, this should be fixed and, at that point, +## the time-consuming on-the-fly uppercasing should be removed again. +awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' '$input_fa_ref' > ref_upper.fa && +#set $input_fa_ref = 'ref_upper.fa' + #set $section = $sec_restrict @PREPARE_TARGETS_FILE@ @PREPARE_REGIONS_FILE@