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annotate Sambamba_merge.xml @ 0:305a4f796bd3 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 19:11:44 +0000
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305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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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"/>
305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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7 <command><![CDATA[
305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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8 sambamba merge
305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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9 -l $compression_level
305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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10 '${output}'
305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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11 #for $infile in $input_bam:
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12 '${infile}'
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13 #end for
305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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14 --nthreads \${GALAXY_SLOTS:-8}
305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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15 ]]></command>
305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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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"/>
305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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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"/>
305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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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"/>
305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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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"/>
305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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33 </test>
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34 </tests>
305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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35 <help>
305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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36 <![CDATA[
305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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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.
305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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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>
305a4f796bd3 planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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43 <expand macro="citations" />
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44 </tool>