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planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
author bgruening
date Mon, 10 Feb 2025 19:12:27 +0000
parents 480c9d4c8957
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480c9d4c8957 planemo upload for repository https://github.com/biod/sambamba commit 13ed0b409cf2c5de007e0a6fa93391cbbb21795d
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1 <tool id="sambamba_merge" name="Sambamba merge" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
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2 <description>Merge several BAM files into one</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"/>
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7 <command><![CDATA[
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8 sambamba merge
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9 -l $compression_level
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10 '${output}'
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11 #for $infile in $input_bam:
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12 '${infile}'
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13 #end for
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14 --nthreads \${GALAXY_SLOTS:-8}
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15 ]]></command>
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16 <inputs>
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17 <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"/>
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18 <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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19 </inputs>
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20 <outputs>
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21 <data name="output" format_source="input_files"/>
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22 </outputs>
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23 <tests>
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24 <test expect_num_outputs="1">
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25 <param name="input_bam" value="qname_sorted.bam,qname_sorted.bam"/>
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26 <param name="compression_level" value="5"/>
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27 <output name="output" file="qname_sorted_merged.bam" lines_diff="4"/>
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28 </test>
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29 <test expect_num_outputs="1">
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30 <param name="input_bam" value="coordinate_sorted.bam,coordinate_sorted.bam"/>
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31 <param name="compression_level" value="5"/>
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32 <output name="output" file="coordinate_sorted_merged.bam" lines_diff="4"/>
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33 </test>
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34 </tests>
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35 <help>
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36 <![CDATA[
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37
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38 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.
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39
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40 SAM headers are merged automatically like in Picard merging tool.
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41 ]]>
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42 </help>
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43 <expand macro="citations" />
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44 </tool>