From 1e92a91ecb06bf89bed83898d63323a23866c248 Mon Sep 17 00:00:00 2001
From: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Date: Mon, 23 Dec 2024 04:21:38 +0000
Subject: [PATCH] Updating tools/bcftools from version 1.15.1 to 1.21

---
 tools/bcftools/bcftools_call.xml      |  2 +-
 tools/bcftools/bcftools_consensus.xml |  2 +-
 tools/bcftools/bcftools_mpileup.xml   |  2 +-
 tools/bcftools/bcftools_norm.xml      |  2 +-
 tools/bcftools/bcftools_stats.xml     |  2 +-
 tools/bcftools/macros.xml             | 10 +++++-----
 6 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/tools/bcftools/bcftools_call.xml b/tools/bcftools/bcftools_call.xml
index f9f7f892000..6f00411dce4 100644
--- a/tools/bcftools/bcftools_call.xml
+++ b/tools/bcftools/bcftools_call.xml
@@ -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>
     <macros>
         <token name="@EXECUTABLE@">call</token>
diff --git a/tools/bcftools/bcftools_consensus.xml b/tools/bcftools/bcftools_consensus.xml
index 4d7b2e32767..231ff51499b 100644
--- a/tools/bcftools/bcftools_consensus.xml
+++ b/tools/bcftools/bcftools_consensus.xml
@@ -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[
diff --git a/tools/bcftools/bcftools_mpileup.xml b/tools/bcftools/bcftools_mpileup.xml
index cde3ecd171b..bb818d97f85 100644
--- a/tools/bcftools/bcftools_mpileup.xml
+++ b/tools/bcftools/bcftools_mpileup.xml
@@ -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>
     <macros>
         <token name="@EXECUTABLE@">mpileup</token>
diff --git a/tools/bcftools/bcftools_norm.xml b/tools/bcftools/bcftools_norm.xml
index aaf65c979a4..b97f977d651 100644
--- a/tools/bcftools/bcftools_norm.xml
+++ b/tools/bcftools/bcftools_norm.xml
@@ -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[
diff --git a/tools/bcftools/bcftools_stats.xml b/tools/bcftools/bcftools_stats.xml
index 66bed896f50..db782ed0897 100644
--- a/tools/bcftools/bcftools_stats.xml
+++ b/tools/bcftools/bcftools_stats.xml
@@ -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[
diff --git a/tools/bcftools/macros.xml b/tools/bcftools/macros.xml
index 564fbd2aab6..03352a9a6df 100644
--- a/tools/bcftools/macros.xml
+++ b/tools/bcftools/macros.xml
@@ -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>
@@ -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>