# HG changeset patch
# User bgruening
# Date 1739214731 0
# Node ID 707d1578e0ecd04ba490c0cbbe7480b63a6c4a46

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

diff -r 000000000000 -r 707d1578e0ec Sambamba_flagstat.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Sambamba_flagstat.xml	Mon Feb 10 19:12:11 2025 +0000
@@ -0,0 +1,45 @@
+<tool id="sambamba_flagstat" name="Sambamba flagstat" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
+    <description>Retrieving flag statistics from BAM file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        sambamba flagstat 
+        '${input_bam}'
+        --nthreads \${GALAXY_SLOTS:-4}
+        > $output
+    ]]></command>
+    <inputs>
+        <param name="input_bam" type="data" format="bam" label="Input BAM file"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" metadata_source="input_bam"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_bam" value="1.bam" ftype="bam"/>
+            <output name="output" md5="7df76f07273f8e35c542831a3f8c4dde"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+Sambamba_flagstat outputs statistics drawn from read flags.
+
+The first line contains numbers of QC-passed and QC-failed reads. Then come pairs of numbers, the former for QC-passed reads, the latter for QC-failed ones:
+    - duplicates
+    - mapped reads (plus percentage relative to the numbers from the first line)
+    - reads with 'is_paired' flag set
+    - paired reads which are first mates
+    - paired reads which are second mates
+    - paired reads with 'proper_pair' flag set (plus percentage relative to the numbers of QC-passed/failed reads with 'is_paired' flag set)
+    - paired reads where both mates are mapped
+    - paired reads where read itself is unmapped but mate is mapped
+    - paired reads where mate is mapped to a different chromosome
+    - the same as previous but mapping quality is not less than 5
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r 707d1578e0ec macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Feb 10 19:12:11 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 707d1578e0ec test-data/1.bam
Binary file test-data/1.bam has changed
diff -r 000000000000 -r 707d1578e0ec test-data/1.coord.sorted.bam
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diff -r 000000000000 -r 707d1578e0ec test-data/1.qname.sorted.bam
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diff -r 000000000000 -r 707d1578e0ec test-data/2.bam
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diff -r 000000000000 -r 707d1578e0ec test-data/2.markdup.bam
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diff -r 000000000000 -r 707d1578e0ec test-data/2.markdup.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.markdup.txt	Mon Feb 10 19:12:11 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 707d1578e0ec test-data/2.markdup_removed.bam
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diff -r 000000000000 -r 707d1578e0ec test-data/coordinate_sorted.bam
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diff -r 000000000000 -r 707d1578e0ec test-data/coordinate_sorted_merged.bam
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diff -r 000000000000 -r 707d1578e0ec test-data/qname_sorted.bam
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diff -r 000000000000 -r 707d1578e0ec test-data/qname_sorted_merged.bam
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