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comparison Sambamba_markdup.xml @ 0:72025d7986cc draft default tip

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planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
author bgruening
date Mon, 10 Feb 2025 19:12:03 +0000
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1 <tool id="sambamba_markdup" name="Sambamba markdup" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
2 <description>Finds and marks duplicate reads in BAM files</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 sambamba markdup
9 $remove_duplicates
10 -l $compression_level
11 '${input_bam}'
12 '${output}'
13 --nthreads \${GALAXY_SLOTS:-4}
14 --tmpdir '\${TMPDIR:-.}'
15 #if $log_out
16 2>&1 | tee '${log}'
17 #end if
18 ]]></command>
19 <inputs>
20 <!-- For deduplication the input bam needs to be coordinate sorted, hence the input file is expected to be coordinate sorted -->
21 <param name="input_bam" type="data" format="bam" label="Input BAM file"/>
22 <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"/>
23 <param argument="--remove-duplicates" type="boolean" truevalue="-r" falsevalue="" label="Remove duplicates instead of just marking them"/>
24 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
25 </inputs>
26 <outputs>
27 <data name="output" format="bam" label="${tool.name} on ${on_string}: Output BAM"/>
28 <data name="log" format="txt" label="${tool.name} on ${on_string}: Output Log">
29 <filter>log_out</filter>
30 </data>
31 </outputs>
32 <tests>
33 <!-- sambamba markdup without dropped reads -->
34 <test expect_num_outputs="2">
35 <param name="input_bam" value="2.bam" ftype="bam"/>
36 <param name="compression_level" value="5"/>
37 <param name="remove_duplicates" value="false"/>
38 <param name="log_out" value="yes"/>
39 <output name="output" file="2.markdup.bam" ftype="bam" lines_diff="4"/>
40 <output name="log" file="2.markdup.txt" ftype="txt"/>
41 </test>
42 <!-- sambamba markdup with dropped reads -->
43 <test expect_num_outputs="1">
44 <param name="input_bam" value="2.bam" ftype="bam"/>
45 <param name="compression_level" value="5"/>
46 <param name="remove_duplicates" value="true"/>
47 <param name="log_out" value="no"/>
48 <output name="output" file="2.markdup_removed.bam" ftype="bam" lines_diff="4"/>
49 </test>
50 </tests>
51 <help>
52 <![CDATA[
53
54 Sambamba_markdup marks (by default) or removes duplicate reads. To determine whether a read is a duplicate or not, the same criteria as in Picard are used.
55
56 ]]>
57 </help>
58 <expand macro="citations"/>
59 </tool>