# HG changeset patch
# User iuc
# Date 1750337908 0
# Node ID 762f63d4e25dbafd913f5baa49c66ace00d9a9a3
# Parent  6856f8a01905867cc5b0a78fb5e847d6002749bf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit c508c3af0f4121dcc38e0be63db00a604e997b8a

diff -r 6856f8a01905 -r 762f63d4e25d macros.xml
--- a/macros.xml	Mon Nov 20 22:14:28 2023 +0000
+++ b/macros.xml	Thu Jun 19 12:58:28 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 6856f8a01905 -r 762f63d4e25d samtools_bedcov.xml
--- a/samtools_bedcov.xml	Mon Nov 20 22:14:28 2023 +0000
+++ b/samtools_bedcov.xml	Thu Jun 19 12:58:28 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_bedcov" name="Samtools bedcov" version="2.0.4" profile="@PROFILE@">
+<tool id="samtools_bedcov" name="Samtools bedcov" version="2.0.5" profile="@PROFILE@">
     <description>calculate read depth for a set of genomic intervals</description>
     <macros>
         <import>macros.xml</import>
@@ -73,21 +73,25 @@
         <test>
             <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
             <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
-            <param name="countdel" value="-j" />
+            <param name="countdel" value="true" />
             <output name="output" file="samtools_bedcov_out2.tab" />
         </test>
         <!-- 5) Testing argument -g -->
         <test>
             <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
             <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_out5.tab" />
         </test>
         <!-- 6) Testing argument -G -->
         <test>
             <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
             <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_out6.tab" />
         </test>
         <!-- 7) Testing depth threshold -d -->