# HG changeset patch
# User iuc
# Date 1750337984 0
# Node ID c05afbeaf42d97e27ed2601e1d179b082af35394
# Parent  d2df79922531d01d8e616ba1464a072380cf2065
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit c508c3af0f4121dcc38e0be63db00a604e997b8a

diff -r d2df79922531 -r c05afbeaf42d macros.xml
--- a/macros.xml	Sun Sep 08 03:26:03 2024 +0000
+++ b/macros.xml	Thu Jun 19 12:59:44 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 $flags = 0
@@ -220,6 +220,7 @@
     <xml name="citations">
         <citations>
             <citation type="doi">10.1093/gigascience/giab008</citation>
+            <citation type="doi">10.1093/bioinformatics/btr076</citation>
         </citations>
     </xml>
     <xml name="version_command">
diff -r d2df79922531 -r c05afbeaf42d samtools_fixmate.xml
--- a/samtools_fixmate.xml	Sun Sep 08 03:26:03 2024 +0000
+++ b/samtools_fixmate.xml	Thu Jun 19 12:59:44 2025 +0000
@@ -61,13 +61,13 @@
         <!--    test_cmd($opts,out=>'fixmate/4_reverse_read_pp_equal.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/4_reverse_read_pp_equal.sam -");-->
         <test>
             <param name="bamfile" value="5_ct.sam" ftype="sam" />
-            <param name="tempcigar" value="-c" />
+            <param name="tempcigar" value="true" />
             <output name="output" file="5_ct.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
         </test>
         <!--    test_cmd($opts,out=>'fixmate/5_ct.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/5_ct.sam -");-->
         <test>
             <param name="bamfile" value="6_ct_replace.sam" ftype="sam" />
-            <param name="tempcigar" value="-c" />
+            <param name="tempcigar" value="true" />
             <output name="output" file="6_ct_replace.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
         </test>
         <!--    test_cmd($opts,out=>'fixmate/6_ct_replace.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/6_ct_replace.sam -");-->