# HG changeset patch
# User iuc
# Date 1750338018 0
# Node ID 229ba92a3b55d3910c73e17d2f040c756acb7f4b
# Parent  40fa6c24010532a10591fcf794202127b760ea87
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit c508c3af0f4121dcc38e0be63db00a604e997b8a

diff -r 40fa6c240105 -r 229ba92a3b55 macros.xml
--- a/macros.xml	Sun Sep 08 03:26:14 2024 +0000
+++ b/macros.xml	Thu Jun 19 13:00:18 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 40fa6c240105 -r 229ba92a3b55 samtools_markdup.xml
--- a/samtools_markdup.xml	Sun Sep 08 03:26:14 2024 +0000
+++ b/samtools_markdup.xml	Thu Jun 19 13:00:18 2025 +0000
@@ -103,13 +103,13 @@
         <!-- 2) -->
         <test expect_num_outputs="1">
             <param name="bamfile" value="2_remove_dups.sam" ftype="sam"  />
-            <param name="remove" value="-r" />
+            <param name="remove" value="true" />
             <output name="output" file="2_remove_dups.expected.bam" ftype="bam" lines_diff="4" />
         </test>
         <!-- 3) -->
         <test expect_num_outputs="1">
             <param name="bamfile" value="3_mark_supp_dup.bam" ftype="bam" />
-            <param name="supp" value="-S" />
+            <param name="supp" value="true" />
             <output name="output" file="3_mark_supp_dup.expected.bam" ftype="bam" lines_diff="4" />
             <assert_command>
                 <has_text text="samtools sort" negate="true"/>
@@ -118,14 +118,18 @@
         <!-- 4) test stats output -->
         <test expect_num_outputs="2">
             <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
-            <param name="stats" value="yes" />
+            <section name="output_options">
+                <param name="stats" value="yes" />
+            </section>
             <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" />
             <output name="stats_output" file="stats.txt" lines_diff="2" />
         </test>
         <!-- 5) check that stderr is not swallowed w test data from fixmate  -->
         <test expect_exit_code="1" expect_failure="true">
             <param name="bamfile" value="3_two_read_mapped.sam" ftype="sam" />
-            <param name="stats" value="yes"/>
+            <section name="output_options">
+                <param name="stats" value="yes"/>
+            </section>
             <assert_stderr>
                 <has_line line="samtools markdup: error, no MC tag. Please run samtools fixmate on file first."/>
                 <has_line line="samtools markdup: error, unable to assign pair hash key."/>
@@ -135,7 +139,7 @@
         <test expect_num_outputs="1">
             <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
             <param name="odist" value="10" />
-            <param name="existing_tags" value="-c" />
+            <param name="existing_tags" value="true" />
             <output name="output" file="6_markdup.expected.bam" ftype="bam" lines_diff="4" />
         </test>
         <!-- 7) check new mode s -->
@@ -153,7 +157,11 @@
         <!-- 9) test sam format -->
         <test expect_num_outputs="1">
             <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
-            <param name="select_oformat" value="SAM" />
+            <section name="output_options">
+                <conditional name="output_format">
+                    <param name="select_oformat" value="SAM" />
+                </conditional>
+            </section>
             <output name="output" file="9_markdup.expected.sam" ftype="sam" lines_diff="4" />
         </test>
         <!-- 10) essentially the same as test 9 (just converted input to sorted bam .. but telling Galaxy its qname sorted)
@@ -161,7 +169,11 @@
                 ie. the qname_sorted bam is not converted implicitly -->
         <test expect_num_outputs="1">
             <param name="bamfile" value="1_markdup.qname_sorted.bam" ftype="qname_sorted.bam" />
-            <param name="select_oformat" value="SAM" />
+            <section name="output_options">
+                <conditional name="output_format">
+                    <param name="select_oformat" value="SAM" />
+                </conditional>
+            </section>
             <output name="output" file="9_markdup.expected.sam" lines_diff="4" />
             <assert_command>
                 <has_text text="samtools sort"/>
@@ -171,8 +183,12 @@
         <!-- 11) test cram format -->
         <test expect_num_outputs="1">
             <param name="bamfile" value="10_markdup.sam" ftype="sam"/>
-            <param name="select_oformat" value="CRAM" />
-            <param name="ref_file" value="test.fa" />
+            <section name="output_options">
+                <conditional name="output_format">
+                    <param name="select_oformat" value="CRAM" />
+                    <param name="ref_file" value="test.fa" />
+                </conditional>
+            </section>
             <output name="output" file="11_markdup.expected.cram" ftype="cram" compare="sim_size" delta="250"/>
             <assert_command>
                 <has_text text="samtools sort"/>