annotate Sambamba_merge.xml @ 0:480c9d4c8957 draft default tip

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

<tool id="sambamba_merge" name="Sambamba merge" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
    <description>Merge several BAM files into one</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command><![CDATA[
        sambamba merge
            -l $compression_level
            '${output}'
            #for $infile in $input_bam:
                '${infile}'
            #end for
            --nthreads \${GALAXY_SLOTS:-8}
    ]]></command>
    <inputs>
        <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"/>
        <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"/>
    </inputs>
    <outputs>
        <data name="output" format_source="input_files"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_bam" value="qname_sorted.bam,qname_sorted.bam"/>
            <param name="compression_level" value="5"/> 
            <output name="output" file="qname_sorted_merged.bam" lines_diff="4"/>
        </test>
        <test expect_num_outputs="1">
            <param name="input_bam" value="coordinate_sorted.bam,coordinate_sorted.bam"/>
            <param name="compression_level" value="5"/>  
            <output name="output" file="coordinate_sorted_merged.bam" lines_diff="4"/>
        </test>
    </tests>
    <help>
<![CDATA[

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.

SAM headers are merged automatically like in Picard merging tool.
]]>
    </help>
    <expand macro="citations" />
</tool>