# HG changeset patch
# User iuc
# Date 1750337917 0
# Node ID 3d5853a84711a3242d911eb230704e31f15f3842
# Parent  26b4f9f98aca17ddecf58f3c9c71a091bbbe283c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit c508c3af0f4121dcc38e0be63db00a604e997b8a

diff -r 26b4f9f98aca -r 3d5853a84711 macros.xml
--- a/macros.xml	Sun Sep 08 03:25:24 2024 +0000
+++ b/macros.xml	Thu Jun 19 12:58:37 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 26b4f9f98aca -r 3d5853a84711 samtools_calmd.xml
--- a/samtools_calmd.xml	Sun Sep 08 03:25:24 2024 +0000
+++ b/samtools_calmd.xml	Thu Jun 19 12:58:37 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_calmd" name="Samtools calmd" version="2.0.4" profile="@PROFILE@">
+<tool id="samtools_calmd" name="Samtools calmd" version="2.0.5" profile="@PROFILE@">
     <description>recalculate MD/NM tags</description>
     <macros>
         <import>macros.xml</import>
@@ -62,22 +62,34 @@
     </outputs>
     <tests>
         <test>
-            <param name="use_baq" value="" />
-            <param name="option_sets" value="default" />
+            <conditional name="baq_settings">
+                <param name="use_baq" value="" />
+            </conditional>
+            <conditional name="option_set">
+                <param name="option_sets" value="default" />
+            </conditional>
             <param name="input" value="phiX.bam"/>
-            <param name="addref_select" value="history" />
-            <param name="ref" value="phiX.fasta" />
+            <conditional name="addref_cond">
+                <param name="addref_select" value="history" />
+                <param name="ref" value="phiX.fasta" />
+            </conditional>
             <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" lines_diff="4" />
         </test>
         <test>
-            <param name="use_baq" value="-r" />
-            <param name="extended_baq" value="true" />
-            <param name="option_sets" value="advanced" />
-            <param name="change_identical" value="true" />
-            <param name="adjust_mq" value="50" />
+            <conditional name="baq_settings">
+                <param name="use_baq" value="-r" />
+                <param name="extended_baq" value="true" />
+            </conditional>
+            <conditional name="option_set">
+                <param name="option_sets" value="advanced" />
+                <param name="change_identical" value="true" />
+                <param name="adjust_mq" value="50" />
+            </conditional>
             <param name="input" value="phiX.bam"/>
-            <param name="addref_select" value="history" />
-            <param name="ref" value="phiX.fasta" />
+            <conditional name="addref_cond">
+                <param name="addref_select" value="history" />
+                <param name="ref" value="phiX.fasta" />
+            </conditional>
             <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" lines_diff="4" />
         </test>
     </tests>