diff ivar_trim.xml @ 16:28e4bcbc86e7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 51d656555f9635bb8988f9eec904ee66657736e1

--- a/ivar_trim.xml	Sat Mar 25 12:53:12 2023 +0000
+++ b/ivar_trim.xml	Wed Apr 19 08:31:08 2023 +0000
@@ -40,12 +40,7 @@
         #end if
         -q $min_qual
         -s $window_width
-        ## since v1.4 ivar trim *almost* supports piping its output, but
-        ## unfortunately still writes *some* regular messages to stdout,
-        ## so we need to stick writing to an intermediate file for now and
-        ## want to unify the output stream
-        -p trimmed 1>&2 &&
-        samtools sort -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o trimmed.sorted.bam trimmed.bam
+        | samtools sort -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o trimmed.sorted.bam -
     ]]></command>
     <inputs>
         <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>