# HG changeset patch
# User iuc
# Date 1762952387 0
# Node ID 5ec5265307257c3392e42beb09e4d055e470f56d
# Parent  48bbbcb692ceb20d27f6a8d5eb092cd8ffef497d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_view commit 19dd8b645a77899ff98d139d79de824a23f416bb

diff -r 48bbbcb692ce -r 5ec526530725 macros.xml
--- a/macros.xml	Thu Jun 19 13:02:07 2025 +0000
+++ b/macros.xml	Wed Nov 12 12:59:47 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@">1.21</token>
-    <token name="@VERSION_SUFFIX@">0</token>
-    <token name="@PROFILE@">22.05</token>
+    <token name="@TOOL_VERSION@">1.22</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 48bbbcb692ce -r 5ec526530725 samtools_view.xml
--- a/samtools_view.xml	Thu Jun 19 13:02:07 2025 +0000
+++ b/samtools_view.xml	Wed Nov 12 12:59:47 2025 +0000
@@ -321,12 +321,9 @@
                     <param name="quality" type="integer" argument="-q" optional="true" min="0" label="Filter by quality" help="Skip alignments with MAPQ smaller than INT." />
                     <param name="library" type="text" argument="-l" optional="true" label="Filter by library" help="Only output alignments in library STR" />
                     <param name="cigarcons" type="integer" argument="-m" optional="true" min="0" label="Filter by number of CIGAR bases consuming query sequence" help="Only output alignments with number of CIGAR bases consuming query sequence greater than or equal INT." />
-                    <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set">
-                        <expand macro="flag_options" />
-                    </param>
-                    <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set">
-                        <expand macro="flag_options" />
-                    </param>
+                    <!-- Use macro for inclusive and axclusive flags -->
+                    <expand macro="inclusive_filter_macro" token_argument="-f"/>
+                    <expand macro="exclusive_filter_macro" token_argument="-F"/>
                     <param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set">
                         <expand macro="flag_options" />
                     </param>