# HG changeset patch
# User iuc
# Date 1750337935 0
# Node ID 772919943459bf04b4f97e437d34a76d835b3ed7
# Parent  971dc85e944184daceae78151149054031d97ac2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_depth commit c508c3af0f4121dcc38e0be63db00a604e997b8a

diff -r 971dc85e9441 -r 772919943459 macros.xml
--- a/macros.xml	Mon Nov 20 22:14:44 2023 +0000
+++ b/macros.xml	Thu Jun 19 12:58:55 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 971dc85e9441 -r 772919943459 samtools_depth.xml
--- a/samtools_depth.xml	Mon Nov 20 22:14:44 2023 +0000
+++ b/samtools_depth.xml	Thu Jun 19 12:58:55 2025 +0000
@@ -135,19 +135,25 @@
                 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
             </conditional>
             <param name="input_bams" value="eboVir3.bam" ftype="bam" />
-            <param name="header" value="true" />
+            <section name="output_options">
+                <param name="header" value="true" />
+            </section>
             <output name="output" file="samtools_depth_out5.tab" />
         </test>
         <!-- 6) Tetsing argument -g -->
         <test>
             <param name="input_bams" value="eboVir3.bam" ftype="bam" />
-            <param name="required_flags" value="2,16,64" />
+            <section name="additional_options">
+                <param name="required_flags" value="2,16,64" />
+            </section>
             <output name="output" file="samtools_depth_out6.tab" />
         </test>
         <!-- 7) Tetsing argument -G -->
         <test>
             <param name="input_bams" value="eboVir3.bam" ftype="bam" />
-            <param name="skipped_flags" value="2,16,64" />
+            <section name="additional_options">
+                <param name="skipped_flags" value="2,16,64" />
+            </section>
             <output name="output" file="samtools_depth_out7.tab" />
         </test>
     </tests>