# HG changeset patch
# User bgruening
# Date 1739214763 0
# Node ID a348429b6fec65b0b4e99390b5636627e328e16c
# Parent  6c916a5a6afb2ab227e464466a7ea128a44187a6
planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9

diff -r 6c916a5a6afb -r a348429b6fec Sambamba_markdup.xml
--- a/Sambamba_markdup.xml	Wed Jun 12 15:01:25 2024 +0000
+++ b/Sambamba_markdup.xml	Mon Feb 10 19:12:43 2025 +0000
@@ -12,29 +12,39 @@
                '${output}'
             --nthreads \${GALAXY_SLOTS:-4}
             --tmpdir '\${TMPDIR:-.}'
+            #if $log_out
+                2>&1 | tee '${log}'
+            #end if
     ]]></command>
     <inputs>
         <!-- For deduplication the input bam needs to be coordinate sorted, hence the input file is expected to be coordinate sorted -->
         <param name="input_bam" type="data" format="bam" label="Input BAM file"/>
         <param argument="--compression-level" type="integer" value="5" min="0" max="9" label="Level of compression for merged BAM file, number from 0 to 9"/>
         <param argument="--remove-duplicates" type="boolean" truevalue="-r" falsevalue="" label="Remove duplicates instead of just marking them"/>
+        <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
     </inputs>
     <outputs>
-        <data name="output" format="bam"/>
+        <data name="output" format="bam" label="${tool.name} on ${on_string}: Output BAM"/>
+        <data name="log" format="txt" label="${tool.name} on ${on_string}: Output Log">
+            <filter>log_out</filter>
+        </data>
     </outputs>
     <tests>
         <!-- sambamba markdup without dropped reads -->
-        <test expect_num_outputs="1">
+        <test expect_num_outputs="2">
             <param name="input_bam" value="2.bam" ftype="bam"/>
             <param name="compression_level" value="5"/>
             <param name="remove_duplicates" value="false"/>
+            <param name="log_out" value="yes"/>
             <output name="output" file="2.markdup.bam" ftype="bam" lines_diff="4"/>
+            <output name="log" file="2.markdup.txt" ftype="txt"/>
         </test>
         <!-- sambamba markdup with dropped reads -->
         <test expect_num_outputs="1">
             <param name="input_bam" value="2.bam" ftype="bam"/>
             <param name="compression_level" value="5"/>
             <param name="remove_duplicates" value="true"/>
+            <param name="log_out" value="no"/>
             <output name="output" file="2.markdup_removed.bam" ftype="bam" lines_diff="4"/>
         </test>
     </tests>
diff -r 6c916a5a6afb -r a348429b6fec macros.xml
--- a/macros.xml	Wed Jun 12 15:01:25 2024 +0000
+++ b/macros.xml	Mon Feb 10 19:12:43 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.0.1</token>
-    <token name="@SUFFIX_VERSION@">1</token>
+    <token name="@SUFFIX_VERSION@">2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="1.0.1">sambamba</requirement>
diff -r 6c916a5a6afb -r a348429b6fec test-data/2.markdup.bam
Binary file test-data/2.markdup.bam has changed
diff -r 6c916a5a6afb -r a348429b6fec test-data/2.markdup.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.markdup.txt	Mon Feb 10 19:12:43 2025 +0000
@@ -0,0 +1,13 @@
+
+sambamba 1.0.1
+ by Artem Tarasov and Pjotr Prins (C) 2012-2023
+    LDC 1.39.0 / DMD v2.109.1 / LLVM17.0.6 / bootstrap LDC - the LLVM D compiler (1.39.0)
+
+finding positions of the duplicate reads in the file...
+  sorted 0 end pairs
+     and 4 single ends (among them 0 unmatched pairs)
+  collecting indices of duplicate reads...   done in 0 ms
+  found 3 duplicates
+collected list of positions in 0 min 0 sec
+marking duplicates...
+collected list of positions in 0 min 0 sec
diff -r 6c916a5a6afb -r a348429b6fec test-data/2.markdup_removed.bam
Binary file test-data/2.markdup_removed.bam has changed