# HG changeset patch
# User iuc
# Date 1750338031 0
# Node ID a7617eb92baffbeac7c11fcb9e33d5c50c611b4d
# Parent  cae2794d2deb8811bee23bb1e85219f1dfc0b55c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_merge commit c508c3af0f4121dcc38e0be63db00a604e997b8a

diff -r cae2794d2deb -r a7617eb92baf macros.xml
--- a/macros.xml	Sun Sep 08 03:26:24 2024 +0000
+++ b/macros.xml	Thu Jun 19 13:00:31 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 cae2794d2deb -r a7617eb92baf samtools_merge.xml
--- a/samtools_merge.xml	Sun Sep 08 03:26:24 2024 +0000
+++ b/samtools_merge.xml	Thu Jun 19 13:00:31 2025 +0000
@@ -110,8 +110,8 @@
         <!--Merge 4 - merge all presented on the command line, combine PG and RG rather than dedup -->
         <test>
             <param name="bamfiles" value="test_input_1_a.bam,test_input_1_b.bam" />
-            <param name="idrg" value="-c" />
-            <param name="idpg" value="-p" />
+            <param name="idrg" value="true" />
+            <param name="idpg" value="true" />
             <output name="output" file="4.merge.expected.bam" ftype="bam" lines_diff="16" />
         </test>
         <!-- Merge 5 - ID and SN with regex in them (probably not necessary for the galaxy tool because just different input) -->
diff -r cae2794d2deb -r a7617eb92baf test-data/1.merge.expected.bam
Binary file test-data/1.merge.expected.bam has changed
diff -r cae2794d2deb -r a7617eb92baf test-data/2.merge.expected.bam
Binary file test-data/2.merge.expected.bam has changed
diff -r cae2794d2deb -r a7617eb92baf test-data/3.merge.expected.bam
Binary file test-data/3.merge.expected.bam has changed
diff -r cae2794d2deb -r a7617eb92baf test-data/4.merge.expected.bam
Binary file test-data/4.merge.expected.bam has changed
diff -r cae2794d2deb -r a7617eb92baf test-data/5.merge.expected.bam
Binary file test-data/5.merge.expected.bam has changed
diff -r cae2794d2deb -r a7617eb92baf test-data/6.merge.expected.bam
Binary file test-data/6.merge.expected.bam has changed
diff -r cae2794d2deb -r a7617eb92baf test-data/rebuild_output_bams.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rebuild_output_bams.sh	Thu Jun 19 13:00:31 2025 +0000
@@ -0,0 +1,6 @@
+samtools merge -s 1 -f 1.merge.expected.bam <(samtools sort -O sam test_input_1_a.sam) <(samtools sort -O sam test_input_1_b.sam)  <(samtools sort -O sam test_input_1_c.sam)
+samtools merge -s 1 -f 2.merge.expected.bam test_input_1_a.bam test_input_1_b.bam test_input_1_c.bam
+samtools merge -s 1 -f 3.merge.expected.bam test_input_1_b.bam 
+samtools merge -s 1 -f -c -p 4.merge.expected.bam test_input_1_a.bam test_input_1_b.bam
+samtools merge -s 1 -f 5.merge.expected.bam test_input_1_a_regex.sam test_input_1_b_regex.sam
+samtools merge -s 1 -f -L test_input_1_a.bed 6.merge.expected.bam test_input_1_a.bam test_input_1_b.bam test_input_1_c.bam