annotate Sambamba_flagstat.xml @ 0:ce3927af5a8f draft default tip

planemo upload for repository https://github.com/biod/sambamba commit 13ed0b409cf2c5de007e0a6fa93391cbbb21795d

<tool id="sambamba_flagstat" name="Sambamba flagstat" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
    <description>Retrieving flag statistics from BAM file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        sambamba flagstat 
        '${input_bam}'
        --nthreads \${GALAXY_SLOTS:-4}
        > $output
    ]]></command>
    <inputs>
        <param name="input_bam" type="data" format="bam" label="Input BAM file"/>
    </inputs>
    <outputs>
        <data name="output" format="txt" metadata_source="input_bam"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_bam" value="1.bam" ftype="bam"/>
            <output name="output" md5="7df76f07273f8e35c542831a3f8c4dde"/>
        </test>
    </tests>
    <help>
<![CDATA[

Sambamba_flagstat outputs statistics drawn from read flags.

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:
    - duplicates
    - mapped reads (plus percentage relative to the numbers from the first line)
    - reads with 'is_paired' flag set
    - paired reads which are first mates
    - paired reads which are second mates
    - paired reads with 'proper_pair' flag set (plus percentage relative to the numbers of QC-passed/failed reads with 'is_paired' flag set)
    - paired reads where both mates are mapped
    - paired reads where read itself is unmapped but mate is mapped
    - paired reads where mate is mapped to a different chromosome
    - the same as previous but mapping quality is not less than 5

]]>
    </help>
    <expand macro="citations" />
</tool>