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annotate Sambamba_flagstat.xml @ 0:707d1578e0ec 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 19:12:11 +0000
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707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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1 <tool id="sambamba_flagstat" name="Sambamba flagstat" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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2 <description>Retrieving flag statistics from BAM file</description>
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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3 <macros>
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4 <import>macros.xml</import>
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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5 </macros>
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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6 <expand macro="requirements"/>
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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7 <command detect_errors="exit_code"><![CDATA[
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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8 sambamba flagstat
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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9 '${input_bam}'
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10 --nthreads \${GALAXY_SLOTS:-4}
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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11 > $output
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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12 ]]></command>
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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13 <inputs>
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14 <param name="input_bam" type="data" format="bam" label="Input BAM file"/>
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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15 </inputs>
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16 <outputs>
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17 <data name="output" format="txt" metadata_source="input_bam"/>
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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18 </outputs>
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19 <tests>
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20 <test expect_num_outputs="1">
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21 <param name="input_bam" value="1.bam" ftype="bam"/>
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22 <output name="output" md5="7df76f07273f8e35c542831a3f8c4dde"/>
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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23 </test>
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24 </tests>
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25 <help>
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26 <![CDATA[
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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27
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28 Sambamba_flagstat outputs statistics drawn from read flags.
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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29
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30 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:
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31 - duplicates
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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32 - mapped reads (plus percentage relative to the numbers from the first line)
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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33 - reads with 'is_paired' flag set
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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34 - paired reads which are first mates
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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35 - paired reads which are second mates
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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36 - paired reads with 'proper_pair' flag set (plus percentage relative to the numbers of QC-passed/failed reads with 'is_paired' flag set)
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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37 - paired reads where both mates are mapped
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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38 - paired reads where read itself is unmapped but mate is mapped
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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39 - paired reads where mate is mapped to a different chromosome
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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40 - the same as previous but mapping quality is not less than 5
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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41
707d1578e0ec planemo upload for repository https://github.com/biod/sambamba commit 99bb4ed496a9cce79ab0a7e613230cf63a44d9f9
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42 ]]>
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43 </help>
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44 <expand macro="citations" />
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45 </tool>