# HG changeset patch
# User bgruening
# Date 1739214704 0
# Node ID 305a4f796bd33c0afb2ef6ceec0710a084ab0d81

planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9

diff -r 000000000000 -r 305a4f796bd3 Sambamba_merge.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Sambamba_merge.xml	Mon Feb 10 19:11:44 2025 +0000
@@ -0,0 +1,44 @@
+<tool id="sambamba_merge" name="Sambamba merge" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
+    <description>Merge several BAM files into one</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command><![CDATA[
+        sambamba merge
+            -l $compression_level
+            '${output}'
+            #for $infile in $input_bam:
+                '${infile}'
+            #end for
+            --nthreads \${GALAXY_SLOTS:-8}
+    ]]></command>
+    <inputs>
+        <param name="input_bam" type="data" format="qname_sorted.bam,bam" multiple="true" label="Input BAM files to be merged" help="Please note that the sorting order of all input files must be the same"/>
+        <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"/>
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input_files"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_bam" value="qname_sorted.bam,qname_sorted.bam"/>
+            <param name="compression_level" value="5"/> 
+            <output name="output" file="qname_sorted_merged.bam" lines_diff="4"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_bam" value="coordinate_sorted.bam,coordinate_sorted.bam"/>
+            <param name="compression_level" value="5"/>  
+            <output name="output" file="coordinate_sorted_merged.bam" lines_diff="4"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+sambamba_merge is used to merge several sorted BAM files into one. The sorting order of all the files must be the same, and it is maintained in the output file.
+
+SAM headers are merged automatically like in Picard merging tool.
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>
\ No newline at end of file
diff -r 000000000000 -r 305a4f796bd3 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Feb 10 19:11:44 2025 +0000
@@ -0,0 +1,17 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.0.1</token>
+    <token name="@SUFFIX_VERSION@">2</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.0.1">sambamba</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btv098</citation>
+            <yield />
+        </citations>
+    </xml>
+</macros>
diff -r 000000000000 -r 305a4f796bd3 test-data/1.bam
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diff -r 000000000000 -r 305a4f796bd3 test-data/1.coord.sorted.bam
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diff -r 000000000000 -r 305a4f796bd3 test-data/1.qname.sorted.bam
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diff -r 000000000000 -r 305a4f796bd3 test-data/2.bam
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diff -r 000000000000 -r 305a4f796bd3 test-data/2.markdup.bam
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diff -r 000000000000 -r 305a4f796bd3 test-data/2.markdup.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.markdup.txt	Mon Feb 10 19:11:44 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 000000000000 -r 305a4f796bd3 test-data/2.markdup_removed.bam
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diff -r 000000000000 -r 305a4f796bd3 test-data/coordinate_sorted.bam
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diff -r 000000000000 -r 305a4f796bd3 test-data/coordinate_sorted_merged.bam
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diff -r 000000000000 -r 305a4f796bd3 test-data/qname_sorted.bam
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diff -r 000000000000 -r 305a4f796bd3 test-data/qname_sorted_merged.bam
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