diff samtools_merge.xml @ 5:84f122ab14d6 draft default tip

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

--- a/samtools_merge.xml	Mon Aug 15 09:11:35 2022 +0000
+++ b/samtools_merge.xml	Sun Sep 08 03:23:00 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_merge" name="Samtools merge" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="samtools_merge" name="Samtools merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>merge multiple sorted alignment files</description>
     <macros>
         <import>macros.xml</import>
@@ -38,7 +38,7 @@
 samtools merge
 -@ \$addthreads
 -s $seed
-## TODO force overwrite seems necessay (but I do not understand why ...)
+## force overwrite seems necessay (but I do not understand why ...)
 -f
 ## Galaxy provides only default compression
 ## #if $compression == 'levelone'
@@ -52,14 +52,14 @@
 #if $sortby=='name'
     -n
 #end if
-## TODO since galaxy can't represent this as data type at the moment this option is unsupported
+## since galaxy can't represent this as data type at the moment this option is unsupported
 ## -t TAG    The input alignments have been sorted by the value of TAG, then by either position or name (if -n is given).
 #if str($region) != ''
     -R '$region'
 #end if
 ## Attach an RG tag to each alignment. The tag value is inferred from file names.
 ## -r
-## TODO -r makes no sense with the link names, is there some data set metadata (tags,...) that could be used?
+## -r makes no sense with the link names, is there some data set metadata (tags,...) that could be used?
 #if $bed_file:
     -L '$bed_file'
 #end if