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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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72025d7986cc planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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1 <tool id="sambamba_markdup" name="Sambamba markdup" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
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2 <description>Finds and marks duplicate reads in BAM files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
72025d7986cc planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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7 <command detect_errors="exit_code"><![CDATA[
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8 sambamba markdup
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9 $remove_duplicates
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10 -l $compression_level
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11 '${input_bam}'
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12 '${output}'
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13 --nthreads \${GALAXY_SLOTS:-4}
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14 --tmpdir '\${TMPDIR:-.}'
72025d7986cc planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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15 #if $log_out
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16 2>&1 | tee '${log}'
72025d7986cc planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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17 #end if
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18 ]]></command>
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19 <inputs>
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20 <!-- For deduplication the input bam needs to be coordinate sorted, hence the input file is expected to be coordinate sorted -->
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21 <param name="input_bam" type="data" format="bam" label="Input BAM file"/>
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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"/>
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23 <param argument="--remove-duplicates" type="boolean" truevalue="-r" falsevalue="" label="Remove duplicates instead of just marking them"/>
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24 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
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25 </inputs>
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26 <outputs>
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27 <data name="output" format="bam" label="${tool.name} on ${on_string}: Output BAM"/>
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28 <data name="log" format="txt" label="${tool.name} on ${on_string}: Output Log">
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29 <filter>log_out</filter>
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30 </data>
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31 </outputs>
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32 <tests>
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33 <!-- sambamba markdup without dropped reads -->
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34 <test expect_num_outputs="2">
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35 <param name="input_bam" value="2.bam" ftype="bam"/>
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36 <param name="compression_level" value="5"/>
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37 <param name="remove_duplicates" value="false"/>
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38 <param name="log_out" value="yes"/>
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39 <output name="output" file="2.markdup.bam" ftype="bam" lines_diff="4"/>
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40 <output name="log" file="2.markdup.txt" ftype="txt"/>
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41 </test>
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42 <!-- sambamba markdup with dropped reads -->
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43 <test expect_num_outputs="1">
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44 <param name="input_bam" value="2.bam" ftype="bam"/>
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45 <param name="compression_level" value="5"/>
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46 <param name="remove_duplicates" value="true"/>
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47 <param name="log_out" value="no"/>
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48 <output name="output" file="2.markdup_removed.bam" ftype="bam" lines_diff="4"/>
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49 </test>
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50 </tests>
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51 <help>
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52 <![CDATA[
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53
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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.
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55
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56 ]]>
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57 </help>
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58 <expand macro="citations"/>
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59 </tool>