# HG changeset patch
# User iuc
# Date 1725766009 0
# Node ID 818030fa6bbf0e57e03bd2797322cb6d65afaf12
# Parent  bd850490c7f1ca3100ff39a07e92ac53b59a2314
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c

diff -r bd850490c7f1 -r 818030fa6bbf macros.xml
--- a/macros.xml	Mon Nov 20 22:16:50 2023 +0000
+++ b/macros.xml	Sun Sep 08 03:26:49 2024 +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="@TOOL_VERSION@">1.20</token>
     <token name="@VERSION_SUFFIX@">2</token>
-    <token name="@PROFILE@">20.05</token>
+    <token name="@PROFILE@">22.05</token>
     <token name="@FLAGS@"><![CDATA[
         #set $flags = 0
         #if $filter
diff -r bd850490c7f1 -r 818030fa6bbf samtools_split.xml
--- a/samtools_split.xml	Mon Nov 20 22:16:50 2023 +0000
+++ b/samtools_split.xml	Sun Sep 08 03:26:49 2024 +0000
@@ -8,12 +8,11 @@
     <expand macro="version_command"/>
     <command><![CDATA[
     @ADDTHREADS@
-    samtools split -f 'Read_Group_%!.bam'
+    samtools split -f 'Read_Group_%!.bam' --output-fmt 'bam'
     #if $header:
-        -u '${output}:${header}'
-    #else:
-        -u '${output}'
+        -h $header'
     #end if
+    -u '$output'
     -@ \$addthreads
     '$input_bam'
     ]]></command>
@@ -41,7 +40,7 @@
 
 Splits BAM files on readgroups.
 
-This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset.
+This tool is based on ``samtools split`` command. It will generate multiple output datasets for each readgroup from the input dataset.
     ]]></help>
     <expand macro="citations"/>
 </tool>
diff -r bd850490c7f1 -r 818030fa6bbf test-data/phiX_Elephant.bam
Binary file test-data/phiX_Elephant.bam has changed
diff -r bd850490c7f1 -r 818030fa6bbf test-data/phiX_Human.bam
Binary file test-data/phiX_Human.bam has changed
diff -r bd850490c7f1 -r 818030fa6bbf test-data/phiX_Mouse.bam
Binary file test-data/phiX_Mouse.bam has changed
diff -r bd850490c7f1 -r 818030fa6bbf test-data/samtools_split_out.bam
Binary file test-data/samtools_split_out.bam has changed