# HG changeset patch
# User iuc
# Date 1626178414 0
# Node ID db82f928d25e112e8d2f93220d3bccb8de6c9551
# Parent  55cdfc5bb8260aa718e56265232148becb815eee
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c2db6daac834eea9b88388aed840d484544f0786"

diff -r 55cdfc5bb826 -r db82f928d25e featurecounts.xml
--- a/featurecounts.xml	Sat Nov 21 10:21:41 2020 +0000
+++ b/featurecounts.xml	Tue Jul 13 12:13:34 2021 +0000
@@ -1,7 +1,12 @@
-<tool id="featurecounts" name="featureCounts" version="2.0.1" profile="16.04">
+<tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
     <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.0.1</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+    </macros>
+
     <requirements>
-        <requirement type="package" version="2.0.1">subread</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">subread</requirement>
         <requirement type="package" version="1.11">samtools</requirement>
         <requirement type="package" version="8.31">coreutils</requirement>
     </requirements>
@@ -120,7 +125,7 @@
         #end if
 
         #if $extended_parameters.R:
-            && samtools sort -o '$output_bam' -@ \${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" *.featureCounts.bam
+            && samtools sort --no-PG -o '$output_bam' -@ \${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" *.featureCounts.bam
         #end if
         && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}'
     ]]></command>
diff -r 55cdfc5bb826 -r db82f928d25e test-data/output.bam
Binary file test-data/output.bam has changed