Mercurial > repos > devteam > samtools_split

diff samtools_split.xml @ 6:818030fa6bbf draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:26:49 +0000
parents bd850490c7f1
children
line wrap: on
line diff
--- 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>