diff samtools_split.xml @ 7:b6caca6a4ca5 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c

--- a/samtools_split.xml	Mon Aug 15 09:12:10 2022 +0000
+++ b/samtools_split.xml	Sun Sep 08 03:23:35 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_split" name="Samtools split" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="samtools_split" name="Samtools split" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>BAM dataset on readgroups</description>
     <macros>
         <import>macros.xml</import>
@@ -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>