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Updating tools/bcftools from version 1.15.1 to 1.21 #3945

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Updating tools/bcftools from version 1.15.1 to 1.21 #3945

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2 changes: 1 addition & 1 deletion tools/bcftools/bcftools_call.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy5" profile="@PROFILE@">
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
<description>SNP/indel variant calling from VCF/BCF</description>
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Suggested change
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">

<macros>
<token name="@EXECUTABLE@">call</token>
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2 changes: 1 addition & 1 deletion tools/bcftools/bcftools_consensus.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
<expand macro="bio_tools" />
<expand macro="requirements">
<expand macro="samtools_requirement"/>
<requirement type="package" version="5.0.1">gawk</requirement>
<requirement type="package" version="5.3.1">gawk</requirement>
</expand>
<expand macro="version_command" />
<command detect_errors="aggressive"><![CDATA[
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2 changes: 1 addition & 1 deletion tools/bcftools/bcftools_mpileup.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
<description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
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Suggested change
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">

<macros>
<token name="@EXECUTABLE@">mpileup</token>
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2 changes: 1 addition & 1 deletion tools/bcftools/bcftools_norm.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
<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>
<requirement type="package" version="5.3.1">gawk</requirement>
</expand>
<expand macro="version_command" />
<command detect_errors="aggressive"><![CDATA[
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2 changes: 1 addition & 1 deletion tools/bcftools/bcftools_stats.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
<expand macro="requirements">
<expand macro="samtools_requirement"/>
<expand macro="matplotlib_requirement" />
<requirement type="package" version="0.12.0">tectonic</requirement>
<requirement type="package" version="0.15.0">tectonic</requirement>
</expand>
<expand macro="version_command" />
<command detect_errors="aggressive"><![CDATA[
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10 changes: 5 additions & 5 deletions tools/bcftools/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
<macros>
<token name="@TOOL_VERSION@">1.15.1</token>
<token name="@VERSION_SUFFIX@">4</token>
<token name="@TOOL_VERSION@">1.21</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@PROFILE@">20.01</token>
<xml name="bio_tools">
<xrefs>
Expand All @@ -10,15 +10,15 @@
<xml name="requirements">
<requirements>
<requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
<requirement type="package" version="1.15.1">htslib</requirement>
<requirement type="package" version="1.21">htslib</requirement>
<yield />
</requirements>
</xml>
<xml name="samtools_requirement">
<requirement type="package" version="1.15.1">samtools</requirement>
<requirement type="package" version="1.21">samtools</requirement>
</xml>
<xml name="matplotlib_requirement">
<requirement type="package" version="3.5.3">matplotlib</requirement>
<requirement type="package" version="3.10.0">matplotlib</requirement>
</xml>
<xml name="version_command">
<version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
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