Mercurial > repos > iuc > bcftools_norm

comparison bcftools_norm.xml @ 12:9ef2d8eb8c30 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 7ea221c576832871e9e5876d6927887d567d4f98"
author iuc
date Thu, 28 Nov 2019 14:46:09 +0000
parents 35cf715a87e5
children 324ba01cb4d8
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11:998726d0de24 12:9ef2d8eb8c30
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy2">
3 <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> 3 <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>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">norm</token> 5 <token name="@EXECUTABLE@">norm</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <expand macro="requirements"> 8 <expand macro="requirements">
9 <expand macro="samtools_requirement"/> 9 <expand macro="samtools_requirement"/>
10 <!-- gawk only required for current bcftools norm bug workaround
11 Remove once fixed (see command section below -->
12 <requirement type="package" version="5.0.1">gawk</requirement>
10 </expand> 13 </expand>
11 <expand macro="version_command" /> 14 <expand macro="version_command" />
12 <command detect_errors="aggressive"><![CDATA[ 15 <command detect_errors="aggressive"><![CDATA[
13 @PREPARE_ENV@ 16 @PREPARE_ENV@
14 @PREPARE_INPUT_FILE@ 17 @PREPARE_INPUT_FILE@
15 #set $section = $reference_source 18 #set $section = $reference_source
16 @PREPARE_FASTA_REF@ 19 @PREPARE_FASTA_REF@
20
21 ## The next two lines are a workaround for a bug in bcftools norm up to version
22 ## 1.9, which caused indel normalization to be case-sensitive
23 ## see:
24 ## https://github.com/samtools/bcftools/commit/65b211da1f5cdbf1c7c11eb610481a736fa88bda
25 ## https://github.com/samtools/bcftools/commit/77b0a27a156803e382d60651ff94ea0bd95fad0f
26 ## With the next release of bcftools, this should be fixed and, at that point,
27 ## the time-consuming on-the-fly uppercasing should be removed again.
28 awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' '$input_fa_ref' > ref_upper.fa &&
29 #set $input_fa_ref = 'ref_upper.fa'
30
17 #set $section = $sec_restrict 31 #set $section = $sec_restrict
18 @PREPARE_TARGETS_FILE@ 32 @PREPARE_TARGETS_FILE@
19 @PREPARE_REGIONS_FILE@ 33 @PREPARE_REGIONS_FILE@
20 34
21 bcftools @EXECUTABLE@ 35 bcftools @EXECUTABLE@