# HG changeset patch
# User iuc
# Date 1750338092 0
# Node ID e221fe58c2f520c2975151e1b2acaa977f027623
# Parent  541082d03bef5715675a95625f3bb76faa9ab686
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit c508c3af0f4121dcc38e0be63db00a604e997b8a

diff -r 541082d03bef -r e221fe58c2f5 macros.xml
--- a/macros.xml	Sun Sep 08 03:27:04 2024 +0000
+++ b/macros.xml	Thu Jun 19 13:01:32 2025 +0000
@@ -11,8 +11,8 @@
          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@">1.20</token>
-    <token name="@VERSION_SUFFIX@">2</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 $flags = 0
@@ -220,6 +220,7 @@
     <xml name="citations">
         <citations>
             <citation type="doi">10.1093/gigascience/giab008</citation>
+            <citation type="doi">10.1093/bioinformatics/btr076</citation>
         </citations>
     </xml>
     <xml name="version_command">
diff -r 541082d03bef -r e221fe58c2f5 samtools_stats.xml
--- a/samtools_stats.xml	Sun Sep 08 03:27:04 2024 +0000
+++ b/samtools_stats.xml	Thu Jun 19 13:01:32 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_stats" name="Samtools stats" version="2.0.5" profile="@PROFILE@">
+<tool id="samtools_stats" name="Samtools stats" version="2.0.6" profile="@PROFILE@">
     <description>generate statistics for BAM dataset</description>
     <macros>
         <import>macros.xml</import>
@@ -275,7 +275,7 @@
                 <param name="select_region" value="tab"/>
                 <param name="targetregions" value="12_3reads.bed" ftype="tabular" />
             </conditional>
-            <param name="remove_overlaps" value="-p"/>
+            <param name="remove_overlaps" value="true"/>
             <output name="output" file="12.3reads.nooverlap.expected" ftype="tabular" lines_diff="4" />
         </test>
         <!-- test_cmd($opts,out=>'stat/12.3reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_3reads.bed | tail -n+4", exp_fix=>$efix);-->
@@ -300,7 +300,7 @@
                 <param name="select_region" value="tab"/>
                 <param name="targetregions" value="12_2reads.bed" ftype="tabular" />
             </conditional>
-            <param name="remove_overlaps" value="-p"/>
+            <param name="remove_overlaps" value="true"/>
             <output name="output" file="12.2reads.nooverlap.expected" ftype="tabular" lines_diff="4" />
         </test>
         <!-- test_cmd($opts,out=>'stat/12.2reads.nooverlap.expected',cmd=>"$$opts{bin}/samtools stats $$opts{path}/stat/12_overlaps.bam -p -t $$opts{path}/stat/12_2reads.bed | tail -n+4", exp_fix=>$efix);-->