# HG changeset patch
# User iuc
# Date 1762952355 0
# Node ID cc01c0658f6cc38389568e4d0cc2d721057e9ef0
# Parent  09652022e2852b0ac57fef89a4ca2ff904d5a669
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_bedcov commit 19dd8b645a77899ff98d139d79de824a23f416bb

diff -r 09652022e285 -r cc01c0658f6c macros.xml
--- a/macros.xml	Fri Jun 27 10:55:21 2025 +0000
+++ b/macros.xml	Wed Nov 12 12:59:15 2025 +0000
@@ -12,8 +12,8 @@
          version catch up eventually). To find the tools check:
         `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` -->
     <token name="@TOOL_VERSION@">1.22</token>
-    <token name="@VERSION_SUFFIX@">0</token>
-    <token name="@PROFILE@">22.05</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@PROFILE@">24.0</token>
     <token name="@FLAGS@"><![CDATA[
         #set $flags = 0
         #if $filter
@@ -167,6 +167,18 @@
     <xml name="seed_input">
        <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
     </xml>
+
+    <!-- Include/exclude by flags + flag options -->
+    <xml name="inclusive_filter_macro" token_argument="">
+        <param name="inclusive_filter" argument="@ARGUMENT@" type="select" multiple="True" label="Require that these flags are set">
+            <expand macro="flag_options" />
+        </param>
+    </xml>
+    <xml name="exclusive_filter_macro" token_argument="">
+        <param name="exclusive_filter" argument="@ARGUMENT@" type="select" multiple="True" label="Exclude reads with any of the following flags set">
+            <expand macro="flag_options" />
+        </param>
+    </xml>
     <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false">
         <option value="1" selected="@S1@">Read is paired</option>
         <option value="2" selected="@S2@">Read is mapped in a proper pair</option>
diff -r 09652022e285 -r cc01c0658f6c samtools_bedcov.xml
--- a/samtools_bedcov.xml	Fri Jun 27 10:55:21 2025 +0000
+++ b/samtools_bedcov.xml	Wed Nov 12 12:59:15 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_bedcov" name="Samtools bedcov" version="2.0.6" profile="@PROFILE@">
+<tool id="samtools_bedcov" name="Samtools bedcov" version="2.0.7" profile="@PROFILE@">
     <description>calculate read depth for a set of genomic intervals</description>
     <macros>
         <import>macros.xml</import>