# HG changeset patch
# User iuc
# Date 1750338051 0
# Node ID 32f6fffbc3e9dbc198b04e3b547ef1fd8acae7a2
# Parent  b61f5d6a7f2519cd06d29d838cba83a1c794cec4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit c508c3af0f4121dcc38e0be63db00a604e997b8a

diff -r b61f5d6a7f25 -r 32f6fffbc3e9 macros.xml
--- a/macros.xml	Mon Nov 20 22:16:18 2023 +0000
+++ b/macros.xml	Thu Jun 19 13:00:51 2025 +0000
@@ -11,9 +11,9 @@
          please only bump the minor version in order to let the requirement
          version catch up eventually). To find the tools check:
         `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` -->
-    <token name="@TOOL_VERSION@">1.15.1</token>
-    <token name="@VERSION_SUFFIX@">2</token>
-    <token name="@PROFILE@">20.05</token>
+    <token name="@TOOL_VERSION@">1.21</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">22.05</token>
     <token name="@FLAGS@"><![CDATA[
         #set $flags = 0
         #if $filter
@@ -220,6 +220,7 @@
     <xml name="citations">
         <citations>
             <citation type="doi">10.1093/gigascience/giab008</citation>
+            <citation type="doi">10.1093/bioinformatics/btr076</citation>
         </citations>
     </xml>
     <xml name="version_command">
diff -r b61f5d6a7f25 -r 32f6fffbc3e9 samtools_mpileup.xml
--- a/samtools_mpileup.xml	Mon Nov 20 22:16:18 2023 +0000
+++ b/samtools_mpileup.xml	Thu Jun 19 13:00:51 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_mpileup" name="Samtools mpileup" version="2.1.7" profile="@PROFILE@">
+<tool id="samtools_mpileup" name="Samtools mpileup" version="2.1.8" profile="@PROFILE@">
     <description>multi-way pileup of variants</description>
     <macros>
         <import>macros.xml</import>
@@ -187,7 +187,7 @@
                     <param name="limit_by_regions" value="limit"/>
                     <param name="region_paste" value="17:1050-1060" />
                 </conditional>
-                <param name="disable_probabilistic_realignment" value="-B" />
+                <param name="disable_probabilistic_realignment" value="true" />
             </conditional>
             <output name="output_file_pu" file="mpileup.out.3" ftype="pileup" />
         </test>
@@ -221,7 +221,7 @@
             </conditional>
             <conditional name="advanced_options">
                 <param name="advanced_options_selector" value="advanced" />
-                <param name="skip_anomalous_read_pairs" value="-A" />
+                <param name="skip_anomalous_read_pairs" value="true" />
             </conditional>
             <output name="output_file_pu" file="samtools_mpileup_out_2.pileup" ftype="pileup" />
         </test>
@@ -268,7 +268,7 @@
 
 **BAQ (Base Alignment Quality)**
 
-BAQ is the Phred-scaled probability of a read base being misaligned. It greatly helps to reduce false SNPs caused by misalignments. BAQ is calculated using the probabilistic realignment method described in the paper “Improving SNP discovery by base alignment quality”, Heng Li, Bioinformatics, Volume 27, Issue 8 <https://doi.org/10.1093/bioinformatics/btr076>
+BAQ is the Phred-scaled probability of a read base being misaligned. It greatly helps to reduce false SNPs caused by misalignments. BAQ is calculated using the probabilistic realignment method described in the paper “Improving SNP discovery by base alignment quality”, Heng Li, Bioinformatics, Volume 27, Issue 8
 
 BAQ is turned on when a reference file is supplied using the -f option. To disable it, use the -B option.